1VJU

Coproporphyrinogen III oxidase from Leishmania major


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52900.4 ul protein 19 mg/ml, 0.4 ul crystallization buffer: 29% PEG 5000MME, 200 mM Ammonium sulfate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.649α = 86.456
b = 53.734β = 77.126
c = 66.627γ = 61.501
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 2102004-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
11.40164.5595.10.0747.643.85238100116623
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)
1.41.4392.90.512.13.6

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTION1.4014011662258580.15140.180415.325
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]
0.007-0.2870.2810.314-0.06-0.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.124
r_dihedral_angle_4_deg15.844
r_dihedral_angle_3_deg13.563
r_dihedral_angle_1_deg5.979
r_scangle_it5.333
r_scbond_it3.747
r_mcangle_it3.491
r_mcbond_it2.836
r_scangle_other2.689
r_angle_refined_deg2.522
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.124
r_dihedral_angle_4_deg15.844
r_dihedral_angle_3_deg13.563
r_dihedral_angle_1_deg5.979
r_scangle_it5.333
r_scbond_it3.747
r_mcangle_it3.491
r_mcbond_it2.836
r_scangle_other2.689
r_angle_refined_deg2.522
r_mcangle_other2.072
r_scbond_other1.288
r_angle_other_deg1.077
r_mcbond_other0.67
r_symmetry_vdw_refined0.435
r_symmetry_vdw_other0.281
r_nbd_refined0.233
r_nbd_other0.213
r_nbtor_refined0.208
r_xyhbond_nbd_refined0.167
r_chiral_restr0.149
r_symmetry_hbond_refined0.141
r_nbtor_other0.1
r_xyhbond_nbd_other0.031
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4694
Nucleic Acid Atoms
Solvent Atoms644
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHELXphasing
RESOLVEphasing
REFMACrefinement
SHELXDphasing