4NG4 | pdb_00004ng4

Structure of phosphoglycerate kinase (CBU_1782) from Coxiella burnetii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZMR	Homology models of cbu_1782 sequence built on the coordinates of 1ZMR, split into two domains

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Sodium chloride, HEPES, PEG 3000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.148	α = 90
b = 91.568	β = 102.17
c = 88.412	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	CCD	ADSC QUANTUM 315		2011-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.78	50	99.3	0.129	11.3	3.2	30881	30663		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.78	2.85	99.9		0.522	2.4	3.4	1532

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	Homology models of cbu_1782 sequence built on the coordinates of 1ZMR, split into two domains	2.78	43.21	31271	29124	1538	98.05	0.27432	0.27231	0.2704	0.31264	0.3028	RANDOM	38.646

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]
-1.09		1.54	-2.34		4.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.423
r_dihedral_angle_3_deg	16.373
r_dihedral_angle_4_deg	15.595
r_dihedral_angle_1_deg	6.12
r_angle_refined_deg	1.195
r_scangle_it	1.122
r_angle_other_deg	0.845
r_scbond_it	0.732
r_mcangle_it	0.364
r_mcbond_it	0.195
r_chiral_restr	0.063
r_mcbond_other	0.06
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8802
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	84

Software

Software
Software Name	Purpose
CBASS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling