X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C5APDB ENTRY 3C5A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429320% PEG6000, 100 mM potassium thiocyanate, 100 mM citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.0840.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.051α = 90
b = 66.288β = 90
c = 71.776γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2009-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

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
11.265097.90.07323.076.763842625041
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)
11.261.3182.50.2723.42.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3C5A1.2633.156384259322318297.90.156660.155880.17139RANDOM14.02
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.068
r_dihedral_angle_3_deg12.798
r_dihedral_angle_4_deg10.68
r_scangle_it6.463
r_dihedral_angle_1_deg6.177
r_scbond_it3.945
r_mcangle_it2.422
r_mcbond_it1.416
r_angle_refined_deg1.36
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.068
r_dihedral_angle_3_deg12.798
r_dihedral_angle_4_deg10.68
r_scangle_it6.463
r_dihedral_angle_1_deg6.177
r_scbond_it3.945
r_mcangle_it2.422
r_mcbond_it1.416
r_angle_refined_deg1.36
r_nbtor_refined0.307
r_nbd_refined0.213
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.129
r_symmetry_hbond_refined0.09
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.008
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 Atoms1972
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms34

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling