5D7R | pdb_00005d7r

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KZN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	296	40-43% MPD_P1K_P3350, 100 mM Mops/Na-Hepes, 100 mM Divalents

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.192	α = 90
b = 55.514	β = 100.65
c = 51.114	γ = 90

Symmetry
Space Group	C 1 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	IMAGE PLATE	RIGAKU RAXIS IV++		2012-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.55	31.34	84.8	0.043	13.3	3.31		48610

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	1.55	1.61	72.7		0.326	2.5	2.56	4152

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	1KZN	1.55	31.34	46160	2445	84.79	0.1828	0.1808	0.1933	0.2197	0.2292	RANDOM	24.962

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]
-0.85		-0.78	0.34		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.399
r_dihedral_angle_4_deg	17.95
r_dihedral_angle_3_deg	13.994
r_dihedral_angle_1_deg	5.788
r_mcangle_it	2.719
r_angle_refined_deg	2.426
r_mcbond_it	1.912
r_mcbond_other	1.892
r_angle_other_deg	1.193
r_chiral_restr	0.161
r_bond_refined_d	0.027
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3058
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
d*TREK	data reduction