X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NZLPDB ENTRY 2NZL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5CRYSTALLISATION WAS PERFORMED BY THE HANGING DROP VAPOR DIFFUSION METHOD, USING A PRECIPITANT SOLUTION CONTAINING 200 MM NACL, 100 MM MMT AT PH 7.5, AND 15% (W/V) POLYETHYLENE GLYCOL 1000
Crystal Properties
Matthews coefficientSolvent content
3.0759.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.69α = 90
b = 138.69β = 90
c = 186.84γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCD2007-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.847.41000.097435742

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 2NZL2.8446.734139321791000.2070.2050.25RANDOM38.1
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]
-0.18-0.180.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.126
r_dihedral_angle_3_deg17.131
r_dihedral_angle_4_deg16.628
r_dihedral_angle_1_deg5.639
r_scangle_it1.744
r_angle_refined_deg1.182
r_scbond_it1.109
r_mcangle_it0.844
r_mcbond_it0.652
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.126
r_dihedral_angle_3_deg17.131
r_dihedral_angle_4_deg16.628
r_dihedral_angle_1_deg5.639
r_scangle_it1.744
r_angle_refined_deg1.182
r_scbond_it1.109
r_mcangle_it0.844
r_mcbond_it0.652
r_nbtor_refined0.302
r_nbd_refined0.195
r_symmetry_vdw_refined0.164
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.111
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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_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 Atoms10344
Nucleic Acid Atoms
Solvent Atoms33
Heterogen Atoms188

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing