3TNB | pdb_00003tnb

Crystal structure of GkaP mutant G209D/R230H from Geobacillus kaustophilus HTA426

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ORW	PDB ENTRY 3ORW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	287	13% PEG 8000, 8% ethylene glycol, 2% glycerol, 0.05M sodium hepes pH7.3, vapor diffusion, hanging drop, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.293	α = 90
b = 88.8	β = 98.86
c = 89.314	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX-225		2010-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	1.000	SSRF	BL17U

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	1.6	50	99.7	0.056	12.9	7.2		103659

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	1.6	1.66	100		0.459		7	10359

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3ORW	1.6	50	103600	5175	99.68	0.1781	0.1774	0.18	0.1919	0.19	RANDOM	24.3437

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]
-0.43		-1.05	0.01		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.906
r_dihedral_angle_4_deg	17.953
r_dihedral_angle_3_deg	13.526
r_dihedral_angle_1_deg	5.565
r_scangle_it	2.488
r_scbond_it	1.402
r_angle_refined_deg	1.071
r_mcangle_it	1.001
r_mcbond_it	0.521
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.906
r_dihedral_angle_4_deg	17.953
r_dihedral_angle_3_deg	13.526
r_dihedral_angle_1_deg	5.565
r_scangle_it	2.488
r_scbond_it	1.402
r_angle_refined_deg	1.071
r_mcangle_it	1.001
r_mcbond_it	0.521
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5102
Nucleic Acid Atoms
Solvent Atoms	709
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.