4C50 | pdb_00004c50

Crystal Structure of the Catalase-Peroxidase (KatG) D137S mutant from Mycobacterium Tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CCA	PDB ENTRY 2CCA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		100 MM SODIUM ACETATE, PH 4.6, 6% PEG 4000, AND 0.17 MM N-DODECYL-BETA-D-MALTOSIDE

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.59	α = 90
b = 150.59	β = 90
c = 157.35	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2011-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	2.5	75.3	99.9	0.13	8.7	6.2		62942		6

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	2.5	2.56	100		0.39	3.9	6.5

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 2CCA	2.5	75.41	59676	3188	99.75	0.26605	0.26363	0.27	0.31113	0.31	RANDOM	34.25

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]
-0.06			-0.06		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.612
r_dihedral_angle_4_deg	15.825
r_dihedral_angle_3_deg	15.714
r_dihedral_angle_1_deg	5.774
r_mcangle_it	4.068
r_mcbond_it	2.492
r_mcbond_other	2.491
r_scbond_it	2.123
r_angle_refined_deg	1.426
r_angle_other_deg	0.833
r_chiral_restr	0.075
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11048
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing