4R43 | pdb_00004r43

Crystal Structure Analysis of MTB PEPCK

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	0.1 M sodium acetate pH 4.6,30% PEG 300 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.358	α = 90
b = 124.696	β = 90
c = 121.466	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		PIXEL	DECTRIS PILATUS 6M		2013-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.979402	BESSY	14.1

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	1.8	47.55	99.7	0.053	24.24			72592		-3	43.447

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	2.16	2.29	99		0.326	10.05

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	3DTB	1.8	47.55	68999	3632	99.83	0.2088	0.207	0.2108	0.2431	0.2471	RANDOM	36.15

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]
-0.67			0.26		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.977
r_dihedral_angle_4_deg	17.165
r_dihedral_angle_3_deg	16.637
r_dihedral_angle_1_deg	7.036
r_angle_refined_deg	1.946
r_angle_other_deg	1.168
r_chiral_restr	0.117
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4644
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	62

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction