2NZJ | pdb_00002nzj

The crystal structure of REM1 in complex with GDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G3Y	pdb entries 2G3Y, 2GJS, 2DPX
experimental model	PDB	2GJS	pdb entries 2G3Y, 2GJS, 2DPX
experimental model	PDB	2DPX	pdb entries 2G3Y, 2GJS, 2DPX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.7	293	34 % (w/v) PEG3350, 0.26M NaCl, 0.1 M HEPES, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.64	α = 90
b = 102.284	β = 90
c = 165.565	γ = 90

Symmetry
Space Group	P 21 21 21

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		2006-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	30	98.2		3.5		25510

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	99.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entries 2G3Y, 2GJS, 2DPX	2.5	29	24187	24187	1284	97.72	0.22728	0.22728	0.2246	0.22	0.27988	0.28	RANDOM	19.796

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]
0.02			-1.74		1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.775
r_dihedral_angle_4_deg	16.082
r_dihedral_angle_3_deg	14.922
r_dihedral_angle_1_deg	6.662
r_scangle_it	1.887
r_angle_refined_deg	1.359
r_scbond_it	1.213
r_angle_other_deg	0.925
r_mcangle_it	0.88
r_mcbond_it	0.499
r_symmetry_vdw_other	0.237
r_nbd_refined	0.208
r_nbd_other	0.197
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_refined	0.156
r_symmetry_hbond_refined	0.147
r_metal_ion_refined	0.121
r_mcbond_other	0.094
r_nbtor_other	0.085
r_chiral_restr	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4651
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	118

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing