X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GCYPDB ENTRY 1GCY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5295PEG 6000, tris, sodium acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
238.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.471α = 90
b = 97.601β = 103.63
c = 53.094γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHBent mirror2002-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8110EMBL/DESY, HAMBURGX11

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
11.872595.80.05615.63.72939429394
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)
11.87288.70.2944.53.24909

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 1GCY1.8724.25293942792214701000.193690.193690.191190.2402RANDOM20.144
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]
-0.20.47-0.040.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.326
r_scangle_it3.523
r_scbond_it2.062
r_mcangle_it1.341
r_angle_refined_deg1.318
r_angle_other_deg0.829
r_mcbond_it0.709
r_symmetry_vdw_other0.288
r_symmetry_hbond_refined0.264
r_symmetry_vdw_refined0.253
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.326
r_scangle_it3.523
r_scbond_it2.062
r_mcangle_it1.341
r_angle_refined_deg1.318
r_angle_other_deg0.829
r_mcbond_it0.709
r_symmetry_vdw_other0.288
r_symmetry_hbond_refined0.264
r_symmetry_vdw_refined0.253
r_nbd_other0.247
r_nbd_refined0.214
r_xyhbond_nbd_refined0.199
r_nbtor_other0.085
r_chiral_restr0.084
r_metal_ion_refined0.023
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3044
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
CNSphasing