2B7S

R381K mutant of flavocytochrome c3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82770.1M TrisHCl, 80mM NaCl, 10mM Na fumarate, 15% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6152.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.228α = 90
b = 91.362β = 91.26
c = 78.193γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.21.488SRSPX14.2

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
12.13599.20.11512.6357643547815.504
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1498.34.71765

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 REPLACEMENTTHROUGHOUT1QJD2.123533702176398.530.146780.144120.19671RANDOM15.472
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]
0.16-0.030.74-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.906
r_dihedral_angle_4_deg17.115
r_dihedral_angle_3_deg14.075
r_dihedral_angle_1_deg6.579
r_scangle_it3.524
r_scbond_it2.325
r_angle_refined_deg1.514
r_mcangle_it1.294
r_mcbond_it0.716
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.906
r_dihedral_angle_4_deg17.115
r_dihedral_angle_3_deg14.075
r_dihedral_angle_1_deg6.579
r_scangle_it3.524
r_scbond_it2.325
r_angle_refined_deg1.514
r_mcangle_it1.294
r_mcbond_it0.716
r_nbtor_refined0.294
r_symmetry_vdw_refined0.283
r_nbd_refined0.236
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.167
r_chiral_restr0.116
r_metal_ion_refined0.061
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms4185
Nucleic Acid Atoms
Solvent Atoms773
Heterogen Atoms234

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing