X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LITPDB Entry 1LIT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829360% 2-methyl-2,4-pentanediol, 10mM calcium chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.38α = 90
b = 69.94β = 136.46
c = 76.69γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-18B1.00Photon FactoryBL-18B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1252.792.3209362093612.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1182.2

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 1LIT252.7199241992410120.140160.140160.138130.1792RANDOM25.338
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]
-1.2-1.59-0.18-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.159
r_scangle_it4.506
r_scbond_it3.073
r_mcangle_it1.804
r_angle_refined_deg1.702
r_mcbond_it1.15
r_angle_other_deg0.904
r_symmetry_vdw_other0.301
r_nbd_other0.264
r_nbd_refined0.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.159
r_scangle_it4.506
r_scbond_it3.073
r_mcangle_it1.804
r_angle_refined_deg1.702
r_mcbond_it1.15
r_angle_other_deg0.904
r_symmetry_vdw_other0.301
r_nbd_other0.264
r_nbd_refined0.225
r_symmetry_hbond_refined0.225
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.161
r_chiral_restr0.116
r_nbtor_other0.09
r_metal_ion_refined0.086
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_gen_planes_other0.007
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2268
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DPSdata reduction
CCP4data scaling
AMoREphasing