2IEC | pdb_00002iec

Crystal Structure of uncharacterized conserved archael protein from Methanopyrus kandleri

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I52	PDB entry 2I52

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	294	100mM Bis-Tris pH 6.5, 500mM magnesium formate dihydrate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.833	α = 90
b = 60.833	β = 90
c = 263.945	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MAR CCD 165 mm		2006-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.979	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.33	20	97.6	0.068	0.071	34.1	15.3		21655			32.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.33	2.46	100		0.103	0.107	24.5	15.5	3164

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 entry 2I52	2.33	8	19509	19509	1057	95.13	0.2066	0.2066	0.2019	0.22	0.2955	0.3	RANDOM	28.935

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]
0.5			0.5		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.228
r_dihedral_angle_4_deg	18.182
r_dihedral_angle_3_deg	17.639
r_dihedral_angle_1_deg	13.744
r_scangle_it	4.2
r_scbond_it	2.643
r_angle_refined_deg	1.722
r_mcangle_it	1.537
r_mcbond_it	0.907
r_xyhbond_nbd_refined	0.327

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3607
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
HKL-2000	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.