X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PD2PDB ENTRY 1PD2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.430% PEG6000, 1% DIOXANE, 5MM DTT, 5MM GSH, 0.05 M TRISHCL PH8.4
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.429α = 90
b = 123.429β = 90
c = 106.273γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2004-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.953999.90.097.83.7579302.3
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)
11.952.0699.90.382.33.5

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 1PD21.9539.1654985293199.90.2010.1980.246RANDOM23.97
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]
0.260.26-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.019
r_dihedral_angle_4_deg13.371
r_dihedral_angle_3_deg10.761
r_dihedral_angle_1_deg2.776
r_scangle_it2.425
r_scbond_it1.561
r_angle_refined_deg1.283
r_mcangle_it1.21
r_mcbond_it0.74
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.019
r_dihedral_angle_4_deg13.371
r_dihedral_angle_3_deg10.761
r_dihedral_angle_1_deg2.776
r_scangle_it2.425
r_scbond_it1.561
r_angle_refined_deg1.283
r_mcangle_it1.21
r_mcbond_it0.74
r_nbtor_refined0.309
r_symmetry_vdw_refined0.202
r_nbd_refined0.198
r_symmetry_hbond_refined0.181
r_xyhbond_nbd_refined0.132
r_chiral_restr0.094
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms6369
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing