X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AGEPDB entry 2AGE with ligand and solvent removed

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8155

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.388α = 90
b = 63.588β = 90
c = 68.849γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.00000ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.2846.6396.270.0750.0759.33.15987059870-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.281.3551.90.4750.4751.72.2

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2AGE with ligand and solvent removed1.2846.635986959869302796.270.1250.1250.1240.158inherited from PDB entry 2AGE8.963
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]
0.83-0.74-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.459
r_dihedral_angle_4_deg20.84
r_sphericity_free16.795
r_dihedral_angle_3_deg10.63
r_sphericity_bonded7.134
r_scangle_it6.747
r_dihedral_angle_1_deg6.679
r_scbond_it5.464
r_rigid_bond_restr5.198
r_mcangle_it4.354
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.459
r_dihedral_angle_4_deg20.84
r_sphericity_free16.795
r_dihedral_angle_3_deg10.63
r_sphericity_bonded7.134
r_scangle_it6.747
r_dihedral_angle_1_deg6.679
r_scbond_it5.464
r_rigid_bond_restr5.198
r_mcangle_it4.354
r_mcbond_it3.455
r_mcbond_other2.264
r_angle_refined_deg1.742
r_angle_other_deg0.933
r_nbd_refined0.386
r_symmetry_vdw_other0.325
r_symmetry_hbond_refined0.283
r_nbd_other0.264
r_xyhbond_nbd_refined0.22
r_metal_ion_refined0.143
r_chiral_restr0.125
r_nbtor_other0.094
r_symmetry_vdw_refined0.032
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1648
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms6

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
REFMACrefinement
CCP4data scaling