X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JX4PDB ENTRY 1JX4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG 4000, HEPES-sodium, calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
3.362.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.955α = 90
b = 101.109β = 97.14
c = 84.124γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B0.9000APS14-ID-B

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
11.95099.20.0394.598435
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)
11.91.9498.70.6713.46523

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 1JX41.95208655586555450899.260.2260.2260.224590.25255RANDOM15.648
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]
-0.08-0.231.38-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.04
r_scangle_it1.741
r_angle_refined_deg1.316
r_scbond_it1.061
r_angle_other_deg0.826
r_mcangle_it0.762
r_mcbond_it0.404
r_symmetry_vdw_other0.316
r_symmetry_vdw_refined0.235
r_nbd_other0.211
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.04
r_scangle_it1.741
r_angle_refined_deg1.316
r_scbond_it1.061
r_angle_other_deg0.826
r_mcangle_it0.762
r_mcbond_it0.404
r_symmetry_vdw_other0.316
r_symmetry_vdw_refined0.235
r_nbd_other0.211
r_nbd_refined0.18
r_xyhbond_nbd_refined0.138
r_symmetry_hbond_refined0.111
r_metal_ion_refined0.103
r_chiral_restr0.101
r_nbtor_other0.078
r_bond_refined_d0.007
r_bond_other_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5478
Nucleic Acid Atoms1259
Solvent Atoms501
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing