X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RFNpdb entry 2RFN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION529312% PEG 6000, 1.0 M lithium chloride, 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6553.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.61α = 90
b = 81.97β = 90
c = 127.038γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2005-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
122091.80.05441.64.9711689723515-3
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)
122.0757.50.261434

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 2RFN219.712306721192231491.870.22070.21490.2737RANDOM31.4478
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]
1.76-2.951.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.195
r_dihedral_angle_3_deg14.308
r_dihedral_angle_4_deg12.595
r_dihedral_angle_1_deg4.717
r_scangle_it1.959
r_mcangle_it1.277
r_scbond_it1.217
r_angle_refined_deg1.202
r_mcbond_it0.727
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.195
r_dihedral_angle_3_deg14.308
r_dihedral_angle_4_deg12.595
r_dihedral_angle_1_deg4.717
r_scangle_it1.959
r_mcangle_it1.277
r_scbond_it1.217
r_angle_refined_deg1.202
r_mcbond_it0.727
r_nbtor_refined0.3
r_nbd_refined0.181
r_symmetry_vdw_refined0.15
r_xyhbond_nbd_refined0.123
r_symmetry_hbond_refined0.109
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2228
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms39

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
AMoREphasing