3H65 | pdb_00003h65

The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme in Complex with Methylenetetrahydromethanopterin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F46	PDB ENTRY 3F46

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	283	50% MPD, 100mM Tris-HCl, 100mM Ammonium dihydrogen phosphate, 1mM DTT, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.63	α = 90
b = 97.63	β = 90
c = 165.75	γ = 90

Symmetry
Space Group	I 41 2 2

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	Dynamically bendable mirror	2008-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9919	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	2.15	48.81	95.1	0.041	17.4	3.6		21096		-3	52.333

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	2.15	2.3	85.8		0.424	3.6	3.5	12007

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3F46	2.15	48.81	21095	1084	95.09	0.171	0.17	0.17	0.203	0.21	RANDOM	48.549

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]
0.64			0.64		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.084
r_dihedral_angle_4_deg	20.038
r_dihedral_angle_3_deg	15.926
r_dihedral_angle_1_deg	5.504
r_scangle_it	3.605
r_scbond_it	2.298
r_angle_refined_deg	1.74
r_mcangle_it	1.243
r_mcbond_it	0.825
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.084
r_dihedral_angle_4_deg	20.038
r_dihedral_angle_3_deg	15.926
r_dihedral_angle_1_deg	5.504
r_scangle_it	3.605
r_scbond_it	2.298
r_angle_refined_deg	1.74
r_mcangle_it	1.243
r_mcbond_it	0.825
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.11
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2601
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	103

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
REFMAC	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.