6HZL | pdb_00006hzl

Crystal structure of redox-inhibited phosphoribulokinase from Synechococcus sp. (strain PCC 6301), osmate derivative

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	277	20 % PEG-3350, 200 mM ammonium formate

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.432	α = 90
b = 141.432	β = 90
c = 206.563	γ = 120

Symmetry
Space Group	H 3 2

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		2017-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.13937	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.77	49.33	100	0.226	0.228	0.03	0.999	17.4	51.9		20468			75

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	2.77	2.92	100		2.465	2.517	0.502	0.706		23.3

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	SAD	THROUGHOUT	2.77	30	19429	1017	99.86	0.2363	0.2352	0.23	0.2589	0.26	RANDOM	114.536

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	0.04		0.07		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.024
r_dihedral_angle_4_deg	15.268
r_dihedral_angle_3_deg	13.362
r_dihedral_angle_1_deg	4.57
r_angle_refined_deg	0.897
r_angle_other_deg	0.687
r_chiral_restr	0.05
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.024
r_dihedral_angle_4_deg	15.268
r_dihedral_angle_3_deg	13.362
r_dihedral_angle_1_deg	4.57
r_angle_refined_deg	0.897
r_angle_other_deg	0.687
r_chiral_restr	0.05
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4954
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
HKL2Map	phasing
PDB_EXTRACT	data extraction

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.