2GBU | pdb_00002gbu

C6A/C111A/C57A/C146A apo CuZn Superoxide dismutase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HL4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	25% PEG4000, 0.1M Na Cacodylate, 50mM NaAc, 1mM EDTA, 1mM NaN3, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.614	α = 90
b = 34.427	β = 112.17
c = 114.461	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		2004-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	1.092	MAX II	I711

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	20	99.6	0.072			38835	38835	1	1

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	2.11	99		0.212	4.4

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	FOURIER SYNTHESIS	THROUGHOUT	1HL4	2	20	38835	38832	1953	99.61	0.219	0.219	0.217	0.23	0.257	0.27	RANDOM	36.981

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]
-3.87		-1.79	6.28		-3.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.654
r_dihedral_angle_3_deg	11.962
r_dihedral_angle_4_deg	11.012
r_dihedral_angle_1_deg	6.05
r_scangle_it	1.345
r_angle_refined_deg	1.061
r_scbond_it	0.961
r_angle_other_deg	0.66
r_mcangle_it	0.585
r_mcbond_it	0.499
r_symmetry_vdw_other	0.193
r_nbd_refined	0.173
r_nbd_other	0.173
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.125
r_symmetry_hbond_refined	0.113
r_nbtor_other	0.079
r_mcbond_other	0.068
r_symmetry_vdw_refined	0.063
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4002
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing