X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MDFPDB ENTRY 1MDF

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.8267.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.55α = 70.06
b = 74.55β = 79.95
c = 89.9γ = 81.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2872007-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
11.8439.4192.20.087.53.51419862
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)
11.841.9184.50.382.63.36

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 1MDF1.8436.66134825715292.30.2230.2210.252RANDOM27.05
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]
0.37-0.12-0.090.28-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.467
r_dihedral_angle_4_deg19.94
r_dihedral_angle_3_deg13.424
r_dihedral_angle_1_deg6.214
r_scangle_it3.67
r_scbond_it2.431
r_angle_refined_deg1.534
r_mcangle_it1.441
r_mcbond_it0.967
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.467
r_dihedral_angle_4_deg19.94
r_dihedral_angle_3_deg13.424
r_dihedral_angle_1_deg6.214
r_scangle_it3.67
r_scbond_it2.431
r_angle_refined_deg1.534
r_mcangle_it1.441
r_mcbond_it0.967
r_nbtor_refined0.303
r_symmetry_hbond_refined0.207
r_nbd_refined0.206
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.176
r_chiral_restr0.102
r_bond_refined_d0.018
r_gen_planes_refined0.007
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 Atoms7520
Nucleic Acid Atoms
Solvent Atoms1062
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing