X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H2RPDB ENTRY 2H2R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629317% (w/v) PEG 4000, 100 mM Mes buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
20.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.31α = 90
b = 51.261β = 90
c = 58.768γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMAR CCD 165 mm2004-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID1.02336APS32-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.33099.40.0941.67.5305233052314.74
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.321000.3383.57.51515

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 2H2R1.338.632887028870156199.370.169530.169530.167850.20045THIN SHELLS15.865
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]
0.52-0.560.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.961
r_sphericity_free18.203
r_dihedral_angle_4_deg17.542
r_dihedral_angle_3_deg11.692
r_sphericity_bonded7.9
r_scangle_it7.473
r_dihedral_angle_1_deg6.723
r_scbond_it6.069
r_mcangle_it5.828
r_mcbond_it4.997
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.961
r_sphericity_free18.203
r_dihedral_angle_4_deg17.542
r_dihedral_angle_3_deg11.692
r_sphericity_bonded7.9
r_scangle_it7.473
r_dihedral_angle_1_deg6.723
r_scbond_it6.069
r_mcangle_it5.828
r_mcbond_it4.997
r_rigid_bond_restr3.762
r_mcbond_other3.363
r_angle_other_deg2.527
r_angle_refined_deg1.658
r_symmetry_vdw_other0.4
r_xyhbond_nbd_other0.251
r_symmetry_hbond_refined0.237
r_nbd_refined0.236
r_symmetry_vdw_refined0.227
r_nbd_other0.222
r_xyhbond_nbd_refined0.203
r_nbtor_refined0.194
r_chiral_restr0.099
r_nbtor_other0.087
r_metal_ion_refined0.031
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing