3WB0 | pdb_00003wb0

HcgB from Methanocaldococcus jannaschii in complex with light-decomposed FeGP cofactor of [Fe]-hydrogenase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BRC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	20 %(w/v) PEG 8000, 0.1 M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.96	α = 90
b = 119.34	β = 115.14
c = 55.65	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	PIXEL	DECTRIS PILATUS 6M		2012-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	SLS	X10SA

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	1.9	50	94.9	0.085	11.17			46660		-3	30.577

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	87.7		0.323	0.412	2.88

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	3BRC	1.91	47.94	45988	2329	94.26	0.2291	0.2266	0.23	0.2752	0.27	RANDOM	29.9177

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]
-0.08		0.07	0.1		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.394
r_dihedral_angle_3_deg	18.138
r_dihedral_angle_4_deg	17.058
r_dihedral_angle_1_deg	6.166
r_scbond_it	3.177
r_mcangle_it	2.652
r_angle_refined_deg	2.031
r_mcbond_it	1.87
r_chiral_restr	0.131
r_bond_refined_d	0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.394
r_dihedral_angle_3_deg	18.138
r_dihedral_angle_4_deg	17.058
r_dihedral_angle_1_deg	6.166
r_scbond_it	3.177
r_mcangle_it	2.652
r_angle_refined_deg	2.031
r_mcbond_it	1.87
r_chiral_restr	0.131
r_bond_refined_d	0.017
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4956
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms	148

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

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.