X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QPPPDB entry 2QPP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277Protein solution (5 mg/ml Protein, 1:1 ratio Heme, 2% DMSO, 0.050 M Potassium chloride, 0.050 M Tris-HCl pH 7.5) mixed in a 1.5:1 ratio with the Well solution (33% PEG DME 500, 0.020 M Magnesium chloride, 0.10 M HEPES pH 7.5). Cryoprotected with well solution, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5651.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.977α = 90
b = 85.094β = 90
c = 97.846γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focus K-B pair Si plus Pt, Rh coatings2007-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97946APS23-ID-B

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
12.3242.41385.60.08316.26811.624030
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)
12.322.427.40.7150.7761.8752

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMulti-conformer re-refinementTHROUGHOUTPDB entry 2QPP2.6139.0219515100599.30.1610.249RANDOM56.5
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.1
c_scangle_it2.2
c_scbond_it1.66
c_angle_deg1.6
c_mcangle_it1.56
c_mcbond_it1.02
c_improper_angle_d0.95
c_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3552
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms86

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing