X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GPMPDB ENTRY 1GPM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.2 M AMMONIUM ACETATE 0.1 M BIS-TRIS PH 5.5 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3840.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.68α = 90
b = 120.88β = 106.43
c = 47.32γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2007-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.420960.1411.524.13144662
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)
12.42.592.40.562.963.88

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1GPM2.419.771370373396.10.2060.2030.261RANDOM16.35
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]
0.060.61-0.370.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.269
r_dihedral_angle_4_deg21.629
r_dihedral_angle_3_deg16.053
r_dihedral_angle_1_deg5.997
r_scangle_it2.55
r_scbond_it1.516
r_angle_refined_deg1.227
r_mcangle_it0.954
r_mcbond_it0.55
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.269
r_dihedral_angle_4_deg21.629
r_dihedral_angle_3_deg16.053
r_dihedral_angle_1_deg5.997
r_scangle_it2.55
r_scbond_it1.516
r_angle_refined_deg1.227
r_mcangle_it0.954
r_mcbond_it0.55
r_nbtor_refined0.302
r_nbd_refined0.186
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.169
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.004
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
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 Atoms2837
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing