X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PZXPDB ENTRY 1PZX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1M MES, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9537.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.304α = 90
b = 42.304β = 90
c = 151.314γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDOXFORD ONYX CCD2007-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA1.54056

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
12.0419.2899.890.0966.54896.4216904
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)
12.042.151000.213.315.512476

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 1PZX2.0419.281685285299.980.185790.182210.25342RANDOM12.23
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]
-0.03-0.030.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.827
r_dihedral_angle_4_deg21.355
r_dihedral_angle_3_deg13.949
r_dihedral_angle_1_deg6.604
r_scangle_it3.653
r_scbond_it2.482
r_angle_refined_deg1.683
r_mcangle_it1.501
r_mcbond_it1.118
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.827
r_dihedral_angle_4_deg21.355
r_dihedral_angle_3_deg13.949
r_dihedral_angle_1_deg6.604
r_scangle_it3.653
r_scbond_it2.482
r_angle_refined_deg1.683
r_mcangle_it1.501
r_mcbond_it1.118
r_nbtor_refined0.302
r_nbd_refined0.212
r_xyhbond_nbd_refined0.194
r_symmetry_vdw_refined0.159
r_symmetry_hbond_refined0.153
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2126
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms18

Software

Software
Software NamePurpose
CrysalisProdata collection
MOLREPphasing
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling