X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2MHBPDB ENTRY 2MHB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION72982.6M ammonium sulfate, 0.01M ammonium phosphate, pH 7.0, LIQUID DIFFUSION, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.4249.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.445α = 90
b = 63.398β = 120.98
c = 102.59γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHOSMIC MIRROR2003-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.82077.70.1733.21.51156044.9
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)
2.82.982.20.3442.11227

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 2MHB2.819.541099656377.720.261570.259950.29349RANDOM32.351
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]
-0.01-0.04-0.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.149
r_dihedral_angle_3_deg17.185
r_dihedral_angle_4_deg15.978
r_mcangle_it10.52
r_mcbond_it7.81
r_dihedral_angle_1_deg3.66
r_scangle_it2.282
r_angle_refined_deg1.448
r_scbond_it1.433
r_symmetry_vdw_refined0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.149
r_dihedral_angle_3_deg17.185
r_dihedral_angle_4_deg15.978
r_mcangle_it10.52
r_mcbond_it7.81
r_dihedral_angle_1_deg3.66
r_scangle_it2.282
r_angle_refined_deg1.448
r_scbond_it1.433
r_symmetry_vdw_refined0.34
r_nbtor_refined0.317
r_nbd_refined0.279
r_xyhbond_nbd_refined0.194
r_symmetry_hbond_refined0.193
r_chiral_restr0.086
r_bond_refined_d0.012
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4272
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing