1N4G

Structure of CYP121, a Mycobacterial P450, in Complex with Iodopyrazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N40 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.3277ammonium sulphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4248.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.717α = 90
b = 78.717β = 90
c = 268.24γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.9EMBL/DESY, HAMBURGX11

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
11.82095.20.0728.14486244862
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8490.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1N401.89.98425784257822841000.205730.205730.205110.21735RANDOM14.21
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg5.394
r_scangle_it4.2
r_scbond_it2.605
r_angle_refined_deg1.865
r_angle_other_deg1.603
r_mcangle_it1.437
r_mcbond_it0.821
r_symmetry_vdw_other0.301
r_nbd_other0.268
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg5.394
r_scangle_it4.2
r_scbond_it2.605
r_angle_refined_deg1.865
r_angle_other_deg1.603
r_mcangle_it1.437
r_mcbond_it0.821
r_symmetry_vdw_other0.301
r_nbd_other0.268
r_symmetry_hbond_refined0.228
r_nbd_refined0.215
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.161
r_chiral_restr0.11
r_nbtor_other0.072
r_bond_refined_d0.022
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2946
Nucleic Acid Atoms
Solvent Atoms539
Heterogen Atoms49

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction