X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1C3DPDB ENTRY 1C3D and structure of C3c

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2293PEG 550 MME, sodium acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2762.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.98α = 90
b = 156.26β = 90
c = 271.2γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9393ESRFID14-4

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
13.339.1299.70.08110.74.53793237818-999-3.7
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)
13.33.599.20.4332.34.5

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 1C3D and structure of C3c3.3403793235817188299.770.233020.230050.28943RANDOM94.4
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]
2.3-0.03-2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.93
r_dihedral_angle_3_deg20.345
r_dihedral_angle_4_deg16.127
r_dihedral_angle_1_deg6.596
r_scangle_it1.06
r_scbond_it0.578
r_mcangle_it0.561
r_angle_refined_deg0.528
r_nbtor_refined0.316
r_mcbond_it0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.93
r_dihedral_angle_3_deg20.345
r_dihedral_angle_4_deg16.127
r_dihedral_angle_1_deg6.596
r_scangle_it1.06
r_scbond_it0.578
r_mcangle_it0.561
r_angle_refined_deg0.528
r_nbtor_refined0.316
r_mcbond_it0.305
r_nbd_refined0.215
r_xyhbond_nbd_refined0.151
r_symmetry_vdw_refined0.131
r_symmetry_hbond_refined0.126
r_chiral_restr0.035
r_gen_planes_refined0.003
r_bond_refined_d0.002
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 Atoms12771
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing