6CWP | pdb_00006cwp

X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide reductase beta subunit (anaerobic)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.2 M magnesium acetate, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.455	α = 90
b = 53.455	β = 90
c = 220.747	γ = 120

Symmetry
Space Group	P 31

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	RAYONIX MX-300		2015-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.92	50	99	0.086	0.095	0.04	8.8	5		53468

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.95	88.1		0.814	0.927	0.429	0.547		3.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.92	50	44358	2367	86.6	0.2077	0.2057	0.21	0.2456	0.25	RANDOM	24.173

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]
0.07	0.03		0.07		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.013
r_dihedral_angle_4_deg	20.291
r_dihedral_angle_3_deg	15.383
r_dihedral_angle_1_deg	5.486
r_angle_refined_deg	1.246
r_angle_other_deg	0.818
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.013
r_dihedral_angle_4_deg	20.291
r_dihedral_angle_3_deg	15.383
r_dihedral_angle_1_deg	5.486
r_angle_refined_deg	1.246
r_angle_other_deg	0.818
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5059
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	4

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	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.