7Z3G | pdb_00007z3g

Crystal structure of the cupredoxin AcoP from Acidithiobacillus ferrooxidans, H166A mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7Z3B7Z3B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293100mM potassium acetate, 10mM potassium chloride, 50mM MES, 50mM Tris, 50mM Hepes, 34-44% PEG3000
Crystal Properties
Matthews coefficientSolvent content
2.0439.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.913α = 90
b = 73.913β = 90
c = 113.87γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.14096.70.99610.47.318289
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.210.477

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7Z3B2.138.531736890595.760.19090.18820.190.24260.24RANDOM40.44
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]
0.380.38-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.878
r_dihedral_angle_4_deg20.969
r_dihedral_angle_3_deg13.722
r_dihedral_angle_1_deg7.439
r_angle_refined_deg1.84
r_angle_other_deg1.466
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.878
r_dihedral_angle_4_deg20.969
r_dihedral_angle_3_deg13.722
r_dihedral_angle_1_deg7.439
r_angle_refined_deg1.84
r_angle_other_deg1.466
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2094
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing