X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NPF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4295Ammonium Sulfate, Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.830.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.223α = 90
b = 28.592β = 106.03
c = 62.841γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2006-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.4521.8498.50.04715.7195871605122
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)
1.451.598.50.247

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1NPF1.619.96153331520484699.160.149050.149050.145790.20644RANDOM16.345
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.316
r_dihedral_angle_4_deg21.999
r_dihedral_angle_3_deg12.919
r_sphericity_free8.573
r_scangle_it6.447
r_sphericity_bonded5.11
r_scbond_it4.825
r_dihedral_angle_1_deg4.497
r_mcangle_it3.748
r_rigid_bond_restr2.947
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.316
r_dihedral_angle_4_deg21.999
r_dihedral_angle_3_deg12.919
r_sphericity_free8.573
r_scangle_it6.447
r_sphericity_bonded5.11
r_scbond_it4.825
r_dihedral_angle_1_deg4.497
r_mcangle_it3.748
r_rigid_bond_restr2.947
r_mcbond_it2.773
r_angle_refined_deg1.135
r_nbtor_refined0.303
r_nbd_refined0.211
r_symmetry_vdw_refined0.17
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.134
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1194
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing