Experiment: 2HLD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E1Q	PDB ENTRY 1E1Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	277	5.5% PEG 6000, 10% glycerol, 4% methanol, 0.05M sodium acetate, 0.5mM nickel sulphate, 0.5mM AMP/PNP, 0.025 mM ADP, 2mM magnesium chloride, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.524	α = 90
b = 294.132	β = 101.67
c = 190.432	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2003-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.0	APS	5ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.6	30	94	0.074	11.7	3.6		346124

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.7	94		0.406	2.6	2	36073

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1E1Q	2.8	20	2	293909	286907	5938	99.94	0.20731	0.20659	0.24412	RANDOM	70.39

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.52		-0.91	-0.42		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.257
r_dihedral_angle_4_deg	18.689
r_dihedral_angle_3_deg	16.083
r_scangle_it	6.462
r_dihedral_angle_1_deg	5.626
r_scbond_it	4.401
r_mcangle_it	2.828
r_mcbond_it	1.645
r_angle_refined_deg	1.346
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.257
r_dihedral_angle_4_deg	18.689
r_dihedral_angle_3_deg	16.083
r_scangle_it	6.462
r_dihedral_angle_1_deg	5.626
r_scbond_it	4.401
r_mcangle_it	2.828
r_mcbond_it	1.645
r_angle_refined_deg	1.346
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.276
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.216
r_metal_ion_refined	0.139
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	72173
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	485

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.