3KGZ | pdb_00003kgz

Crystal structure of a cupin 2 conserved barrel domain protein from Rhodopseudomonas palustris

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	294	100mM Bis-Tris pH 5.5, 19% PEG 3350, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.854	α = 90
b = 80.382	β = 90
c = 110.081	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD		2009-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.85	64.917	99.8	0.099	0.099	17.6	14.6	28776	28718			21.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.95	99.6		0.373	0.373	7	14.6	4114

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.85	20	28718	28638	1451	99.72	0.202	0.199	0.21	0.248	0.25	RANDOM	23.602

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]
-2.01			0.08		1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.663
r_dihedral_angle_4_deg	12.866
r_dihedral_angle_3_deg	12.301
r_dihedral_angle_1_deg	5.86
r_scangle_it	3.614
r_scbond_it	2.362
r_mcangle_it	1.631
r_angle_refined_deg	1.493
r_mcbond_it	0.884
r_angle_other_deg	0.841

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.663
r_dihedral_angle_4_deg	12.866
r_dihedral_angle_3_deg	12.301
r_dihedral_angle_1_deg	5.86
r_scangle_it	3.614
r_scbond_it	2.362
r_mcangle_it	1.631
r_angle_refined_deg	1.493
r_mcbond_it	0.884
r_angle_other_deg	0.841
r_mcbond_other	0.23
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2268
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.