3I95

Crystal structure of E76Q mutant PcyA-biliverdin complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D1EPDB ENTRY 2D1E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.7M ammonium sulfate, 2% PEG 400, 0.1M HEPES (pH 7.0), vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5752.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.681α = 90
b = 95.701β = 90
c = 42.727γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102009-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0000SPring-8BL38B1

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
11.417.9899.40.0556.757594
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)
1.41.4598.40.2956

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 DIFFRACTIONDIFFERENCE FOURIERTHROUGHOUTPDB ENTRY 2D1E1.417.9857590292999.470.1760.1750.192RANDOM16.171
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
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg16.342
r_dihedral_angle_3_deg12.467
r_dihedral_angle_1_deg5.919
r_scangle_it2.486
r_angle_refined_deg1.683
r_scbond_it1.66
r_mcangle_it1.12
r_mcbond_it0.677
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.703
r_dihedral_angle_4_deg16.342
r_dihedral_angle_3_deg12.467
r_dihedral_angle_1_deg5.919
r_scangle_it2.486
r_angle_refined_deg1.683
r_scbond_it1.66
r_mcangle_it1.12
r_mcbond_it0.677
r_nbtor_refined0.303
r_nbd_refined0.202
r_symmetry_vdw_refined0.201
r_symmetry_hbond_refined0.122
r_xyhbond_nbd_refined0.106
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2072
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling