2FER | pdb_00002fer

P450CAM from Pseudomonas putida reconstituted with manganic protoporphyrin IX


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FE6PDB ENTRY 2FE6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42777.5 MG/ML P450, 25 MM POTASSIUM PHOSPHATE, 250 MM KCL, 50 MM TRIS, 13.5-15% PEG 8000, 50 MM DTE, pH 7.40, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3347.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.32α = 90
b = 63.82β = 90
c = 105.44γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARRESEARCH2005-07-23MSINGLE WAVELENGTH
21x-rayM
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1,21.71895.90.0710.612.834721326.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.891.50.3660.313.89

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2FE61.717.594720147201236098.90.1810.1790.180.2250.23RANDOM22.05
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]
0.630.36-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_3_deg13.195
r_dihedral_angle_4_deg12.061
r_dihedral_angle_1_deg5.505
r_scangle_it3.723
r_scbond_it2.297
r_angle_refined_deg1.427
r_mcangle_it1.365
r_mcbond_it0.728
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_3_deg13.195
r_dihedral_angle_4_deg12.061
r_dihedral_angle_1_deg5.505
r_scangle_it3.723
r_scbond_it2.297
r_angle_refined_deg1.427
r_mcangle_it1.365
r_mcbond_it0.728
r_nbtor_refined0.309
r_nbd_refined0.212
r_symmetry_vdw_refined0.193
r_metal_ion_refined0.169
r_xyhbond_nbd_refined0.165
r_symmetry_hbond_refined0.157
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3221
Nucleic Acid Atoms
Solvent Atoms487
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata scaling
CNSphasing