2QF5

High resolution structure of the major periplasmic domain from the cell shape-determining filament MreC (monoclinic form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QF4PDB entry 2QF4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62980.1M Sodium acetate pH 4.6, 0.2M Ammonium sulfate, 12.5% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3848.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.998α = 90
b = 48.283β = 115.32
c = 48.429γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2006-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.2323.8390.30.030.0318.35.27873
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)
12.232.3376.40.1230.12365.1966

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 2QF42.2323.83787036592.720.1970.1940.268RANDOM20.21
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]
2.9-1.19-1.76-2.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.843
r_dihedral_angle_4_deg22.352
r_dihedral_angle_3_deg15.396
r_dihedral_angle_1_deg6.329
r_scangle_it2.393
r_scbond_it1.541
r_angle_refined_deg1.376
r_angle_other_deg0.882
r_mcangle_it0.867
r_mcbond_it0.688
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.843
r_dihedral_angle_4_deg22.352
r_dihedral_angle_3_deg15.396
r_dihedral_angle_1_deg6.329
r_scangle_it2.393
r_scbond_it1.541
r_angle_refined_deg1.376
r_angle_other_deg0.882
r_mcangle_it0.867
r_mcbond_it0.688
r_symmetry_vdw_other0.254
r_nbd_refined0.195
r_symmetry_hbond_refined0.195
r_nbd_other0.19
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.155
r_symmetry_vdw_refined0.145
r_mcbond_other0.124
r_nbtor_other0.086
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1161
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing