3K63 | pdb_00003k63

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

X-RAY DIFFRACTION

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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