X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A15PDB ENTRY 3A15

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729317% (W/V) PEG 2000MME, 0.1M Trizma/HCl, 0.2M calcium acetate, 2%(V/V) butyraldoxime, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7455.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.052α = 76.5
b = 103.931β = 89.46
c = 114.189γ = 87.55
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 2102008-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B21.0000SPring-8BL44B2

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
12.52090.80.0798.8391.9114706-3
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)
2.52.5983.10.2932.0461.910470

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 3A152.519.9112560565691.170.2130.2110.243RANDOM29.332
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]
-3.310.161.583.9-0.09-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.709
r_dihedral_angle_4_deg18.065
r_dihedral_angle_3_deg15.418
r_dihedral_angle_1_deg5.79
r_scangle_it1.354
r_angle_refined_deg1.139
r_scbond_it0.855
r_mcangle_it0.796
r_mcbond_it0.457
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.709
r_dihedral_angle_4_deg18.065
r_dihedral_angle_3_deg15.418
r_dihedral_angle_1_deg5.79
r_scangle_it1.354
r_angle_refined_deg1.139
r_scbond_it0.855
r_mcangle_it0.796
r_mcbond_it0.457
r_nbtor_refined0.296
r_nbd_refined0.191
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.153
r_xyhbond_nbd_refined0.129
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22645
Nucleic Acid Atoms
Solvent Atoms619
Heterogen Atoms392

Software

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