X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YCRPDB ENTRY 1YCR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.530030% PEG300, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
1.9938.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.43α = 90
b = 30.81β = 107.43
c = 70.09γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirror2008-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00SLSX10SA

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
11.83094.50.06915.926003247032
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)
1.8285.10.2236.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1YCR1.824.49223573127196.920.20710.205120.24292RANDOM14.882
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]
-0.09-0.090.06-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.842
r_dihedral_angle_4_deg22.751
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg5.885
r_scangle_it2.575
r_scbond_it1.737
r_mcangle_it1.352
r_angle_refined_deg1.236
r_angle_other_deg0.88
r_mcbond_it0.863
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.842
r_dihedral_angle_4_deg22.751
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg5.885
r_scangle_it2.575
r_scbond_it1.737
r_mcangle_it1.352
r_angle_refined_deg1.236
r_angle_other_deg0.88
r_mcbond_it0.863
r_symmetry_vdw_other0.299
r_nbd_refined0.211
r_nbd_other0.185
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.15
r_mcbond_other0.143
r_symmetry_hbond_refined0.141
r_nbtor_other0.088
r_chiral_restr0.073
r_symmetry_vdw_refined0.05
r_bond_refined_d0.008
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 Atoms1532
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing