X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P71PDB ENTRY 1P71 with nonidentical sidechains pruned back to a common atom

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8292Peg 5000 monomethyl ether, glycerol, tris, jeffamine, potassium chloride, calcium chloride, sodium azide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.7554.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.646α = 90
b = 107.836β = 92.25
c = 83.464γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
12.489993.30.10732332423324-3
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)
12.482.5746.50.3592.2

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 1P71 with nonidentical sidechains pruned back to a common atom2.5252304216900182881.390.2910.2860.338RANDOM28.115
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]
-1.440.09-0.622.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.511
r_scangle_it1.668
r_angle_refined_deg0.927
r_scbond_it0.894
r_mcangle_it0.81
r_mcbond_it0.431
r_nbd_refined0.175
r_symmetry_vdw_refined0.157
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.511
r_scangle_it1.668
r_angle_refined_deg0.927
r_scbond_it0.894
r_mcangle_it0.81
r_mcbond_it0.431
r_nbd_refined0.175
r_symmetry_vdw_refined0.157
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.124
r_chiral_restr0.046
r_bond_refined_d0.005
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2767
Nucleic Acid Atoms1556
Solvent Atoms72
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing