4DP9

The 1.00 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 6.0


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PLCPDB ENTRY 1PLC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62772.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.8332.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.012α = 90
b = 46.354β = 90
c = 57.091γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2002-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1115.9996.90.04519.23.5424814115225.84
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
111.0280.70.263.52.92042

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PLC115.994068639319209696.640.122210.121090.14397RANDOM10.265
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]
0.06-0.01-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.2
r_sphericity_free13.637
r_dihedral_angle_3_deg10.874
r_dihedral_angle_1_deg7.443
r_scangle_it6.921
r_sphericity_bonded6.534
r_scbond_it5.203
r_mcangle_it3.279
r_rigid_bond_restr2.742
r_angle_refined_deg2.663
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.2
r_sphericity_free13.637
r_dihedral_angle_3_deg10.874
r_dihedral_angle_1_deg7.443
r_scangle_it6.921
r_sphericity_bonded6.534
r_scbond_it5.203
r_mcangle_it3.279
r_rigid_bond_restr2.742
r_angle_refined_deg2.663
r_mcbond_it2.528
r_nbd_refined0.573
r_xyhbond_nbd_refined0.504
r_symmetry_hbond_refined0.385
r_nbtor_refined0.329
r_symmetry_vdw_refined0.262
r_chiral_restr0.164
r_metal_ion_refined0.069
r_bond_refined_d0.027
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms738
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms1

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling