X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYPpdb entry 1RYP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 MM MGAC2, 13% MPD, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.11α = 90
b = 301.03β = 113.18
c = 144.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.63097.80.06611.732414731701622
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)
12.62.7990.4952.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1RYP2.6153170163011651585197.960.18940.188110.21396RANDOM61.698
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]
4.2-1.23-5.71.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.02
r_sphericity_free28.94
r_sphericity_bonded16.163
r_dihedral_angle_3_deg13.769
r_dihedral_angle_4_deg13.13
r_dihedral_angle_1_deg5.035
r_long_range_B_refined3.277
r_long_range_B_other3.236
r_mcangle_it2.847
r_mcangle_other2.847
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.02
r_sphericity_free28.94
r_sphericity_bonded16.163
r_dihedral_angle_3_deg13.769
r_dihedral_angle_4_deg13.13
r_dihedral_angle_1_deg5.035
r_long_range_B_refined3.277
r_long_range_B_other3.236
r_mcangle_it2.847
r_mcangle_other2.847
r_scangle_other2.538
r_mcbond_it2.153
r_mcbond_other2.153
r_scbond_it2.085
r_scbond_other2.084
r_rigid_bond_restr1.185
r_angle_refined_deg0.852
r_angle_other_deg0.682
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49370
Nucleic Acid Atoms
Solvent Atoms646
Heterogen Atoms12

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing