X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MBCPDB ENTRY 1MBC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
162932.4M Ammonium Sulfate, 10mM Tris-HCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8734.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.312α = 90
b = 30.618β = 105.74
c = 63.714γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray40CCDMAR CCD 165 mm2007-05-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW14A0.827Photon FactoryAR-NW14A

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
11.215094.70.03315.43.737292-3
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)
1.211.25730.2043.12817

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 1MBC1.2117.1537268187395.710.1440.1420.182RANDOM13.241
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]
0.010.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.17
r_dihedral_angle_4_deg18.297
r_dihedral_angle_3_deg13.825
r_sphericity_free9.663
r_sphericity_bonded5.438
r_scangle_it5.377
r_dihedral_angle_1_deg4.913
r_scbond_it3.913
r_mcangle_it2.871
r_rigid_bond_restr2.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.17
r_dihedral_angle_4_deg18.297
r_dihedral_angle_3_deg13.825
r_sphericity_free9.663
r_sphericity_bonded5.438
r_scangle_it5.377
r_dihedral_angle_1_deg4.913
r_scbond_it3.913
r_mcangle_it2.871
r_rigid_bond_restr2.3
r_mcbond_it2.028
r_angle_refined_deg1.862
r_metal_ion_refined0.586
r_nbtor_refined0.319
r_nbd_refined0.308
r_symmetry_hbond_refined0.166
r_symmetry_vdw_refined0.145
r_chiral_restr0.135
r_xyhbond_nbd_refined0.123
r_bond_refined_d0.019
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1217
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms55

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling