3K63 | pdb_00003k63

X-ray structure of the PF04200 domain from Q9PRA0_UREPA protein of Ureaplasma parvum. NESG target UuR17a.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER PARAFFIN OIL	7.5	291	40% PEG 8000, 0.1M KBr, 0.1M HEPES pH 7.5, MICROBATCH UNDER PARAFFIN OIL, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.557	α = 90
b = 60.557	β = 90
c = 64.716	γ = 120

Symmetry
Space Group	P 32 2 1

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	ADSC QUANTUM 4		2009-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97908	NSLS	X4A

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	2.494	50	99.5	0.089	36.8	11.2	9299	9252

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)
	2.5	2.59	97.9		0.812	3.65	10.6	933

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	2.494	27.538	1.27	9232	426	99.5	0.2147	0.2131	0.2153	0.248	0.241	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.267
f_angle_d	1.639
f_chiral_restr	0.112
f_plane_restr	0.009
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	985
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHELX	model building
RESOLVE	model building
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	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.