X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FAP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293100 mM Tris-HCl buffer (pH 7.0), 200 mM calcium acetate and 20% (w/v) PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.9558.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.546α = 90
b = 127.546β = 90
c = 278.557γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225-HS2019-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
13.1148.61000.9929.514.842250
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.113.230.522

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 REPLACEMENTTHROUGHOUT1FAP3.1148.6540024214299.960.238420.236290.27844RANDOM70.304
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]
1.381.38-2.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.853
r_dihedral_angle_3_deg14.278
r_dihedral_angle_4_deg13.654
r_long_range_B_refined4.563
r_dihedral_angle_1_deg4.515
r_mcangle_it1.731
r_mcbond_it0.948
r_scbond_it0.712
r_angle_refined_deg0.664
r_chiral_restr0.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.853
r_dihedral_angle_3_deg14.278
r_dihedral_angle_4_deg13.654
r_long_range_B_refined4.563
r_dihedral_angle_1_deg4.515
r_mcangle_it1.731
r_mcbond_it0.948
r_scbond_it0.712
r_angle_refined_deg0.664
r_chiral_restr0.054
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_it
r_scangle_other
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 Atoms13335
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms270

Software

Software
Software NamePurpose
XDSdata reduction
MOLREPphasing
REFMACrefinement
Aimlessdata scaling