2YLG

CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: ASCORBATE AND CARBON MONOOXIDE BOUND L16A VARIANT AT 1.05 A RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YL0PDB ENTRY 2YL0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5AMMONIUM SULPHATE, TRIS PH 7.5.
Crystal Properties
Matthews coefficientSolvent content
2.7455.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.64α = 90
b = 53.64β = 90
c = 181.443γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2009-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
11.05451000.0521.5117311711.8
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)
11.051.11000.81.89

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 2YL01.0546.457016729241000.138460.137930.15076RANDOM19.592
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]
-0.68-0.34-0.681.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.833
r_dihedral_angle_4_deg17.908
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg5.094
r_scangle_it4.938
r_scbond_it3.596
r_mcangle_it2.848
r_angle_refined_deg2.042
r_mcbond_it1.886
r_rigid_bond_restr1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.833
r_dihedral_angle_4_deg17.908
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg5.094
r_scangle_it4.938
r_scbond_it3.596
r_mcangle_it2.848
r_angle_refined_deg2.042
r_mcbond_it1.886
r_rigid_bond_restr1.42
r_angle_other_deg1.006
r_mcbond_other0.646
r_chiral_restr0.108
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_gen_planes_other0.004
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms946
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing