5N0G | pdb_00005n0g

Crystal Structure of CobH T85A (precorrin-8x methyl mutase) complexed with C5 allyl-HBA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292.15	20% PEG 8000, 0.2M Calcium acetate hydrate, 0.1M Sodium cacodylate pH6.5, 20% methanol

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.23	α = 90
b = 66.63	β = 99.03
c = 48.92	γ = 90

Symmetry
Space Group	C 1 2 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 2M		2015-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.57	48.38	92.4	0.2	0.279	0.84	2.67	1.815		57377		-3	24.882

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.57	1.61	90.9		0.747	1.022	0.378	0.99	1.793

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.57	48.38	29762	1461	98.81	0.1753	0.1723	0.19	0.2384	0.24	RANDOM	23.096

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]
0.31		0.67	0.04		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.23
r_sphericity_free	21.544
r_dihedral_angle_4_deg	14.721
r_dihedral_angle_3_deg	13.584
r_dihedral_angle_1_deg	6.667
r_sphericity_bonded	6.226
r_rigid_bond_restr	5.647
r_angle_refined_deg	2.731
r_angle_other_deg	1.278
r_chiral_restr	0.172

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.23
r_sphericity_free	21.544
r_dihedral_angle_4_deg	14.721
r_dihedral_angle_3_deg	13.584
r_dihedral_angle_1_deg	6.667
r_sphericity_bonded	6.226
r_rigid_bond_restr	5.647
r_angle_refined_deg	2.731
r_angle_other_deg	1.278
r_chiral_restr	0.172
r_bond_refined_d	0.03
r_gen_planes_refined	0.015
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1530
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	71

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	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.