9FL5 | pdb_00009fl5

compound 3b bound KMT9 crystal structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H1D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.2 M Na3Citrate, 0.1M Tris 7.5
Crystal Properties
Matthews coefficientSolvent content
3.1761.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.293α = 90
b = 110.293β = 90
c = 130.473γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2019-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.3947.7699.90.093128.73993637
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.391.420.613

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.39247.7693564477499.8780.1520.15010.150.17910.178722.124
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]
-0.093-0.047-0.0930.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.266
r_dihedral_angle_3_deg14.282
r_dihedral_angle_2_deg8.557
r_scbond_it7.208
r_scbond_other7.206
r_scangle_it7.203
r_scangle_other7.201
r_lrange_other7.04
r_lrange_it7.03
r_rigid_bond_restr6.982
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.266
r_dihedral_angle_3_deg14.282
r_dihedral_angle_2_deg8.557
r_scbond_it7.208
r_scbond_other7.206
r_scangle_it7.203
r_scangle_other7.201
r_lrange_other7.04
r_lrange_it7.03
r_rigid_bond_restr6.982
r_dihedral_angle_1_deg6.414
r_mcangle_it5.397
r_mcangle_other5.396
r_mcbond_it5.311
r_mcbond_other5.311
r_angle_refined_deg1.744
r_angle_other_deg0.604
r_nbd_refined0.233
r_symmetry_nbd_refined0.214
r_nbd_other0.205
r_symmetry_nbd_other0.188
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_refined0.137
r_xyhbond_nbd_refined0.126
r_chiral_restr0.104
r_symmetry_nbtor_other0.081
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2418
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing