5A4M | pdb_00005a4m

Mechanism of Hydrogen activation by NiFe-hydrogenases

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2		0.2 M NA/K TARTRATE, 20% (W/V) PEG 3350, pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.671	α = 90
b = 97.162	β = 90
c = 182.911	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	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2014-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	1.7	46.9	99.1	0.1	9.8	5.6		181455		-3

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	1.7	1.73	98.2		1.04	1.6	5.5

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	PDB ENTRY 3USC	1.7	91.62	172419	8979	98.94	0.13564	0.13425	0.15	0.16235	0.17	RANDOM	21

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]
-0.01			1.32		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.904
r_dihedral_angle_4_deg	17.443
r_dihedral_angle_3_deg	12.526
r_dihedral_angle_1_deg	6.105
r_scangle_it	4.135
r_angle_refined_deg	2.256
r_scbond_it	2.094
r_angle_other_deg	1.585
r_mcangle_it	1.547
r_mcbond_it	1.058
r_mcbond_other	1.058
r_symmetry_vdw_refined	0.31
r_nbd_refined	0.278
r_xyhbond_nbd_other	0.262
r_nbd_other	0.232
r_nbtor_refined	0.186
r_chiral_restr	0.175
r_symmetry_vdw_other	0.175
r_xyhbond_nbd_refined	0.169
r_symmetry_hbond_refined	0.143
r_metal_ion_refined	0.112
r_nbtor_other	0.099
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_bond_other_d	0.008
r_gen_planes_other	0.005
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13133
Nucleic Acid Atoms
Solvent Atoms	1492
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing