X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q32PDB entry 2Q32

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
2.651.6

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2Q322.6140.96219515100599.3640.2050.2020.256RANDOM65.958
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]
-0.34-1.2161.555
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.971
r_dihedral_angle_4_deg19.242
r_dihedral_angle_3_deg15.542
r_dihedral_angle_1_deg4.47
r_mcangle_it1.234
r_scangle_it1.167
r_angle_refined_deg0.951
r_scbond_it0.859
r_mcbond_it0.732
r_nbtor_refined0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.971
r_dihedral_angle_4_deg19.242
r_dihedral_angle_3_deg15.542
r_dihedral_angle_1_deg4.47
r_mcangle_it1.234
r_scangle_it1.167
r_angle_refined_deg0.951
r_scbond_it0.859
r_mcbond_it0.732
r_nbtor_refined0.29
r_symmetry_hbond_refined0.266
r_nbd_refined0.182
r_symmetry_vdw_refined0.152
r_xyhbond_nbd_refined0.127
r_chiral_restr0.07
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3552
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms86

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling