X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5ZPDB ENTRY 1P5Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52851.0M Sodium Citrate, 100mM Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
1.9938.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.8α = 90
b = 107.5β = 90
c = 110.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.9730960.09110.173622636226
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)
1.97279.40.4583.13.31316

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 1P5Z1.973032619360796.040.211270.206060.25877RANDOM28.641
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]
-0.931.99-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.649
r_dihedral_angle_4_deg22.009
r_dihedral_angle_3_deg18.126
r_dihedral_angle_1_deg6.031
r_scangle_it3.739
r_scbond_it2.559
r_mcangle_it1.762
r_angle_refined_deg1.635
r_mcbond_it1.055
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.649
r_dihedral_angle_4_deg22.009
r_dihedral_angle_3_deg18.126
r_dihedral_angle_1_deg6.031
r_scangle_it3.739
r_scbond_it2.559
r_mcangle_it1.762
r_angle_refined_deg1.635
r_mcbond_it1.055
r_nbtor_refined0.318
r_nbd_refined0.205
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.179
r_symmetry_hbond_refined0.131
r_chiral_restr0.116
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3525
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
SERGUIdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing