5ADU | pdb_00005adu

The 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		6		100 MM BIS-TRIS PH 6.0, 21 % PEG 3350, 200 MM LISO4, 150 MM NACL

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.855	α = 90
b = 98.979	β = 90
c = 185.207	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 2M	MIRRORS	2015-07-04	M	SINGLE WAVELENGTH

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

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	1.1	49.5	95.5	0.16	10.5	12.8		665775		-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	1.1	1.12	92.1		1.5	1.7	12.3

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	1.1	92.78	632387	33298	95.27	0.12693	0.12612	0.14	0.14238	0.15	RANDOM	10.686

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]
0.2					-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.317
r_sphericity_free	18.264
r_dihedral_angle_4_deg	16.302
r_dihedral_angle_3_deg	11.911
r_dihedral_angle_1_deg	6.112
r_sphericity_bonded	5.275
r_rigid_bond_restr	3.035
r_angle_refined_deg	1.866
r_scangle_it	1.662
r_scbond_it	1.403
r_angle_other_deg	1.073
r_mcangle_it	1.054
r_mcbond_it	0.829
r_mcbond_other	0.829
r_symmetry_vdw_refined	0.244
r_xyhbond_nbd_other	0.243
r_metal_ion_refined	0.238
r_nbd_refined	0.229
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.161
r_nbd_other	0.152
r_symmetry_vdw_other	0.139
r_chiral_restr	0.107
r_symmetry_hbond_refined	0.087
r_nbtor_other	0.07
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13163
Nucleic Acid Atoms
Solvent Atoms	1093
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing