2YLD

RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND AT 1.25 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YKZPDB ENTRY 2YKZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5AMMONIUM SULPHATE, TRIS PH 7.5 .
Crystal Properties
Matthews coefficientSolvent content
2.755

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.914α = 90
b = 53.914β = 90
c = 180.864γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRROR2008-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.1SRSPX10.1

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
11.253697.80.08226.64096111.9
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)
11.251.2981.20.193.54.2

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 2YKZ1.2546.6840961217297.630.16260.161170.19RANDOM19.463
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]
-0.54-0.27-0.540.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.113
r_dihedral_angle_4_deg25.427
r_dihedral_angle_3_deg14.667
r_scangle_it6.219
r_dihedral_angle_1_deg4.634
r_scbond_it4.215
r_mcangle_it3.247
r_mcbond_it2.289
r_angle_refined_deg2.09
r_rigid_bond_restr1.479
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.113
r_dihedral_angle_4_deg25.427
r_dihedral_angle_3_deg14.667
r_scangle_it6.219
r_dihedral_angle_1_deg4.634
r_scbond_it4.215
r_mcangle_it3.247
r_mcbond_it2.289
r_angle_refined_deg2.09
r_rigid_bond_restr1.479
r_angle_other_deg0.954
r_mcbond_other0.696
r_chiral_restr0.127
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms949
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing