X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AVDPDB ENTRY 1AVD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52932.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1961.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.01α = 90
b = 81.224β = 92.47
c = 74.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-04-24
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
11.65098.30.0875.5176927
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)
11.61.6695.40.3415.3

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 1AVD1.635.85176927888097.980.19080.18950.2148RANDOM19.6812
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.518
r_dihedral_angle_4_deg25.112
r_dihedral_angle_3_deg15.555
r_dihedral_angle_1_deg6.58
r_scangle_it6.349
r_scbond_it4.228
r_mcangle_it3.05
r_angle_refined_deg2.925
r_mcbond_it1.845
r_chiral_restr0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.518
r_dihedral_angle_4_deg25.112
r_dihedral_angle_3_deg15.555
r_dihedral_angle_1_deg6.58
r_scangle_it6.349
r_scbond_it4.228
r_mcangle_it3.05
r_angle_refined_deg2.925
r_mcbond_it1.845
r_chiral_restr0.222
r_bond_refined_d0.035
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7648
Nucleic Acid Atoms
Solvent Atoms572
Heterogen Atoms324

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data scaling