5OVU | pdb_00005ovu

Cupriavidus metallidurans BPH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OVS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	100 mM sodium acetate pH 4.4, 1.5 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.496	α = 90
b = 96.496	β = 90
c = 75.894	γ = 120

Symmetry
Space Group	P 6

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-F		2015-09-21	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.1	37.9	99.8	0.144	0.997	11.7	9.39		23627

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.22	99.3		1.12	0.796	2.03	9.33

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	5OVS	2.1	37.9	22444	1182	99.84	0.2377	0.23693	0.24	0.25227	0.26	RANDOM	34.597

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]
-1.13	-0.56		-1.13		3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.467
r_dihedral_angle_3_deg	12.51
r_dihedral_angle_4_deg	8.677
r_dihedral_angle_1_deg	5.383
r_long_range_B_refined	2.916
r_long_range_B_other	2.874
r_angle_refined_deg	0.919
r_scangle_other	0.737
r_mcangle_it	0.733
r_mcangle_other	0.733
r_angle_other_deg	0.706
r_scbond_it	0.43
r_scbond_other	0.428
r_mcbond_it	0.414
r_mcbond_other	0.414
r_chiral_restr	0.052
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2859
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing