X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LD9pdb entry 3LD9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5290EBS Wizard 3/4 screen h6: 30% MPD, 25% PEG 1500, 100mM HOAc/NAOAC; protein ButhA.01616.a.A1 PS01176 at 56.3 mg/ml, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.244.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.13α = 90
b = 77.97β = 90
c = 84.13γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-11-11MSINGLE 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
11.95099.20.09115.475.963599235693-324.144
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9593.80.5270.5272.32.72616

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 REPLACEMENTTHROUGHOUTpdb entry 3LD91.9503599233908178699.170.18330.18330.18140.2175RANDOM20.9104
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]
1.34-0.44-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.933
r_dihedral_angle_4_deg14.149
r_dihedral_angle_3_deg12.408
r_dihedral_angle_1_deg5.453
r_angle_refined_deg1.451
r_angle_other_deg0.904
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.933
r_dihedral_angle_4_deg14.149
r_dihedral_angle_3_deg12.408
r_dihedral_angle_1_deg5.453
r_angle_refined_deg1.451
r_angle_other_deg0.904
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3112
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms43

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction