X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JUEPDB accession code 1JUE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42980.4 ul protein 14.1 mg/ml 0.4 ul crystallization buffer, 40% PEG 1000, 0.1M Na Citrate, 0.1M KBr, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
236.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.605α = 90
b = 162.63β = 90
c = 163.07γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-09-05MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.9201ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.9516396.20.1070.10764.476097
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)
11.952.060.4280.4281.8

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 accession code 1JUE1.955075972721583814960.19160.188940.24243RANDOM14.022
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]
-0.781.08-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_4_deg15.886
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg6.255
r_scangle_it2.256
r_scbond_it1.495
r_angle_refined_deg1.326
r_angle_other_deg0.837
r_mcangle_it0.821
r_mcbond_it0.714
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_4_deg15.886
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg6.255
r_scangle_it2.256
r_scbond_it1.495
r_angle_refined_deg1.326
r_angle_other_deg0.837
r_mcangle_it0.821
r_mcbond_it0.714
r_symmetry_vdw_refined0.323
r_symmetry_hbond_refined0.294
r_symmetry_vdw_other0.259
r_nbd_refined0.196
r_nbd_other0.178
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.168
r_mcbond_other0.127
r_nbtor_other0.083
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9572
Nucleic Acid Atoms
Solvent Atoms638
Heterogen Atoms203

Software

Software
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
CCP4data scaling
MOLREPphasing