X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L6MPDB entry 1L6M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52910.2M Ammonium sulfate, 30% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.957.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.908α = 90
b = 114.908β = 90
c = 118.832γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

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
12.882.48990.07729.859.82026920066
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)
12.82.999.50.4055.929.91955

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 entry 1L6M2.847.962026919017102699.020.251080.248270.30397Used same set as previously-determined structure31.185
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]
-0.11-0.110.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.074
r_dihedral_angle_4_deg17.145
r_dihedral_angle_3_deg14.554
r_dihedral_angle_1_deg7.937
r_angle_refined_deg0.941
r_scangle_it0.885
r_angle_other_deg0.792
r_mcangle_it0.541
r_scbond_it0.529
r_mcbond_it0.286
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.074
r_dihedral_angle_4_deg17.145
r_dihedral_angle_3_deg14.554
r_dihedral_angle_1_deg7.937
r_angle_refined_deg0.941
r_scangle_it0.885
r_angle_other_deg0.792
r_mcangle_it0.541
r_scbond_it0.529
r_mcbond_it0.286
r_nbd_other0.18
r_nbtor_refined0.177
r_nbd_refined0.168
r_symmetry_vdw_refined0.152
r_symmetry_vdw_other0.125
r_symmetry_hbond_refined0.109
r_xyhbond_nbd_refined0.097
r_nbtor_other0.078
r_chiral_restr0.056
r_mcbond_other0.03
r_metal_ion_refined0.028
r_bond_other_d0.007
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3911
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms161

Software

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