3PM9

Crystal structure of a Putative dehydrogenase (RPA1076) from Rhodopseudomonas palustris CGA009 at 2.57 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.60M potassium dihydrogen phosphate, 25.00% Glycerol, 0.60M sodium dihydrogen phosphate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.085	α = 90
b = 250.728	β = 90
c = 251.711	γ = 90

Symmetry
Space Group	I 2 2 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	CCD	MARMOSAIC 325 mm CCD		2010-06-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97922,0.97894	SSRL	BL11-1

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	2.57	49.357	98.9	0.114	10.26			144716		-3	52.656

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	2.57	2.66	99.9		0.824	1.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.57	49.357	144702	7270	98.91	0.1948	0.1931	0.2266	RANDOM	39.0054

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]
1.19			-0.79		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.66
r_dihedral_angle_4_deg	13.344
r_dihedral_angle_3_deg	10.123
r_dihedral_angle_1_deg	2.761
r_scangle_it	2.009
r_angle_refined_deg	1.299
r_scbond_it	1.118
r_angle_other_deg	0.88
r_mcangle_it	0.865
r_mcbond_it	0.445

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.66
r_dihedral_angle_4_deg	13.344
r_dihedral_angle_3_deg	10.123
r_dihedral_angle_1_deg	2.761
r_scangle_it	2.009
r_angle_refined_deg	1.299
r_scbond_it	1.118
r_angle_other_deg	0.88
r_mcangle_it	0.865
r_mcbond_it	0.445
r_chiral_restr	0.071
r_mcbond_other	0.058
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20838
Nucleic Acid Atoms
Solvent Atoms	919
Heterogen Atoms	444

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.