X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SMDPDB ENTRY 1SMD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929845% MPD, 0.1M Tris.HCl, 10 mM calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.282α = 90
b = 75.046β = 90
c = 135.013γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 4mirrors2007-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.9777CHESSA1

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
1236.1699.080.1010.10134.25.43653734563140.9
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)
22.0399.30.4180.4187.65.51810

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 1SMD236.163653734563181199.080.1950.177630.175720.21475RANDOM33.573
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.662
r_dihedral_angle_4_deg20.552
r_dihedral_angle_3_deg15.472
r_dihedral_angle_1_deg6.504
r_scangle_it4.227
r_scbond_it2.884
r_mcangle_it1.856
r_angle_refined_deg1.641
r_mcbond_it1.182
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.662
r_dihedral_angle_4_deg20.552
r_dihedral_angle_3_deg15.472
r_dihedral_angle_1_deg6.504
r_scangle_it4.227
r_scbond_it2.884
r_mcangle_it1.856
r_angle_refined_deg1.641
r_mcbond_it1.182
r_nbtor_refined0.312
r_nbd_refined0.204
r_symmetry_vdw_refined0.174
r_symmetry_hbond_refined0.14
r_xyhbond_nbd_refined0.125
r_chiral_restr0.122
r_metal_ion_refined0.103
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3937
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing