X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QPDPDB ENTRY 1QPD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527723% polyethylene glycol 3350, 0.1M NaCl, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7354.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.378α = 90
b = 127.378β = 90
c = 55.619γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54180

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.639.210106

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 1QPD2.633.37962447697.620.199350.19780.23111RANDOM26.737
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]
-0.03-0.02-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.809
r_dihedral_angle_3_deg16.804
r_dihedral_angle_4_deg12.048
r_dihedral_angle_1_deg5.645
r_scangle_it3.165
r_scbond_it2.122
r_mcangle_it1.721
r_angle_refined_deg1.204
r_mcbond_it0.891
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.809
r_dihedral_angle_3_deg16.804
r_dihedral_angle_4_deg12.048
r_dihedral_angle_1_deg5.645
r_scangle_it3.165
r_scbond_it2.122
r_mcangle_it1.721
r_angle_refined_deg1.204
r_mcbond_it0.891
r_nbtor_refined0.305
r_nbd_refined0.183
r_symmetry_hbond_refined0.134
r_xyhbond_nbd_refined0.113
r_symmetry_vdw_refined0.109
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.002
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 Atoms2076
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement