X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K7XPDB ENTRY 3K7X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18BT3792 AT A 20 MG PER ML BUFFERED IN IN 25 MM TRIS-HCL (PH 8.0), 500 MM NACL, 2 MM DTT WITH A RESERVOIR SOLUTION CONSISTING OF 5% GLYCEROL (V/V), 24% (W PER V) POLYETHYLENE GLYCOL 2,000 MONOMETHYL ETHER, 0.25 M SODIUM ACETATE, AND BIS-TRIS-HCL (PH 5.5)
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.1α = 90
b = 44.42β = 101.43
c = 103.05γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MX-300HECOLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) , TOROIDAL FOCUSING MIRROR (RH AND PT)2012-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-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
12.14899.90.1110.44.252497
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)
12.12.2199.90.483.34.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 3K7X2.148.0349817267499.830.21560.213590.25264RANDOM24.111
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]
12.47-21.1-13.731.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.243
r_dihedral_angle_4_deg19.648
r_dihedral_angle_3_deg15.706
r_dihedral_angle_1_deg7.162
r_mcangle_it3.252
r_scbond_it3.071
r_mcbond_it2.425
r_angle_refined_deg1.597
r_chiral_restr0.117
r_bond_refined_d0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.243
r_dihedral_angle_4_deg19.648
r_dihedral_angle_3_deg15.706
r_dihedral_angle_1_deg7.162
r_mcangle_it3.252
r_scbond_it3.071
r_mcbond_it2.425
r_angle_refined_deg1.597
r_chiral_restr0.117
r_bond_refined_d0.014
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6078
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
AutoProcessdata reduction
SCALAdata scaling
PHASERphasing