1PZS | pdb_00001pzs

Crystal Structure of a Cu-Zn Superoxide Dismutase from Mycobacterium tuberculosis at 1.63 resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JCV	PDB ENTRY 1JCV.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG 4000, Ammonium sulfate, zinc chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.04	α = 90
b = 58.42	β = 126.99
c = 51.39	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	MARRESEARCH		2002-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13	0.9755	ESRF	ID13

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	1.634	27.95	96	0.067	13.54	3.62	20248	20248			21.844

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	1.634	1.8	87.9		0.273	5.17	3.27	4640

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 (All)	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 1JCV.pdb	1.63	27.95	20248	19233	1013	98.2	0.15233	0.15233	0.15029	0.16	0.19027	0.2	RANDOM	13.359

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]
0.82		1.19	-0.52		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.233
r_scangle_it	3.475
r_scbond_it	2.123
r_angle_other_deg	1.858
r_mcangle_it	1.484
r_angle_refined_deg	1.356
r_mcbond_it	0.831
r_symmetry_vdw_other	0.328
r_nbd_other	0.253
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.154
r_symmetry_vdw_refined	0.132
r_symmetry_hbond_refined	0.119
r_chiral_restr	0.084
r_nbtor_other	0.084
r_bond_refined_d	0.01
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1204
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing