X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P38PDB entry 1P38

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.629050 mM Hepes pH 7.6, 50 mM CaCl2, 17% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.957.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.461α = 90
b = 87.215β = 90
c = 124.869γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
125098.10.1283387330.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0787.40.5491.82985

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1P38233.8631709168597.110.214560.213110.2421RANDOM30.469
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]
-0.78-0.281.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.953
r_dihedral_angle_3_deg12.38
r_dihedral_angle_1_deg5.133
r_scangle_it1.864
r_scbond_it1.15
r_mcangle_it0.99
r_angle_refined_deg0.982
r_mcbond_it0.581
r_nbtor_refined0.301
r_nbd_refined0.188
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.953
r_dihedral_angle_3_deg12.38
r_dihedral_angle_1_deg5.133
r_scangle_it1.864
r_scbond_it1.15
r_mcangle_it0.99
r_angle_refined_deg0.982
r_mcbond_it0.581
r_nbtor_refined0.301
r_nbd_refined0.188
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.121
r_symmetry_hbond_refined0.105
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2793
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing