1Y0P

Flavocytochrome c3 with mesaconate bound


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277TrisHCl, mesaconate, NaCl, PEG8000, pH 7.8-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5651.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.449α = 90
b = 91.687β = 91.13
c = 78.287γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.10.975SRSPX14.1

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
11.52497.20.048211024869956414.247
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)
1.51.55940.3733.129590

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 REPLACEMENTTHROUGHOUT1QJD1.52494583497897.210.152480.150840.18353RANDOM14.247
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]
0.89-0.120.2-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.117
r_scangle_it3.429
r_scbond_it2.183
r_angle_refined_deg1.511
r_mcangle_it1.344
r_angle_other_deg0.968
r_mcbond_it0.796
r_nbd_refined0.28
r_nbd_other0.257
r_symmetry_vdw_other0.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.117
r_scangle_it3.429
r_scbond_it2.183
r_angle_refined_deg1.511
r_mcangle_it1.344
r_angle_other_deg0.968
r_mcbond_it0.796
r_nbd_refined0.28
r_nbd_other0.257
r_symmetry_vdw_other0.256
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.169
r_chiral_restr0.137
r_nbtor_other0.084
r_metal_ion_refined0.053
r_bond_refined_d0.015
r_gen_planes_other0.011
r_gen_planes_refined0.01
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4217
Nucleic Acid Atoms
Solvent Atoms1249
Heterogen Atoms235

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling