2IQI | pdb_00002iqi

Crystal structure of protein XCC0632 from Xanthomonas campestris, Pfam DUF330

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	294	100mM Hepes, pH 7.5, 20% PEG 4000, 10% isopropanol, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.933	α = 90
b = 103.114	β = 90
c = 121.65	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MAR CCD 165 mm		2006-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID		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	2.7	19.937	99.7	0.146	0.146	14.9	7.3	54597	54433			53

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)
	2.7	2.85	99.9		0.697	0.697	3	7.1	7844

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	2.7	19.89	54405	54389	1548	99.97	0.211	0.209	0.21	0.275	0.27	RANDOM	46.965

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]
-0.13			0.28		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.658
r_dihedral_angle_4_deg	19.846
r_dihedral_angle_3_deg	17.223
r_dihedral_angle_1_deg	7.105
r_scangle_it	3.666
r_scbond_it	2.21
r_angle_refined_deg	1.647
r_mcangle_it	1.395
r_mcbond_it	0.821
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.658
r_dihedral_angle_4_deg	19.846
r_dihedral_angle_3_deg	17.223
r_dihedral_angle_1_deg	7.105
r_scangle_it	3.666
r_scbond_it	2.21
r_angle_refined_deg	1.647
r_mcangle_it	1.395
r_mcbond_it	0.821
r_nbtor_refined	0.313
r_symmetry_hbond_refined	0.242
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.208
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10477
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	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.