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
2.1643.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.76α = 90
b = 44.09β = 95.71
c = 94.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-12-11MSINGLE 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
11.793099.40.11411.76.15216952169
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)
1.791.996.90.6273.35.68138

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 1P5Z1.83046591522599.170.206950.202180.24991RANDOM23.586
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]
1.19-0.21-0.93-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.524
r_dihedral_angle_4_deg18.699
r_dihedral_angle_3_deg16.028
r_dihedral_angle_1_deg5.726
r_scangle_it3.614
r_scbond_it2.704
r_mcangle_it1.71
r_angle_refined_deg1.552
r_mcbond_it1.048
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.524
r_dihedral_angle_4_deg18.699
r_dihedral_angle_3_deg16.028
r_dihedral_angle_1_deg5.726
r_scangle_it3.614
r_scbond_it2.704
r_mcangle_it1.71
r_angle_refined_deg1.552
r_mcbond_it1.048
r_nbtor_refined0.309
r_symmetry_vdw_refined0.221
r_nbd_refined0.209
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.14
r_chiral_restr0.117
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3644
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
SERGUIdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing