X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QLPPDB ENTRY 1QLP DIFFERENCES TO ALA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.62950.1M Na tartarate, 0.1M HEPES, 24% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.34α = 90
b = 92.62β = 90
c = 118.26γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Bent conical Si-mirror (Rh coating)2004-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
1210092.40.07515.593.26251357467
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)
122.0772.90.4152.14480

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 1QLP DIFFERENCES TO ALA2.130.015409251453208695.10.1950.1950.1930.239RANDOM34.229
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]
-1.053.82-2.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.273
r_dihedral_angle_4_deg17.302
r_dihedral_angle_3_deg14.725
r_scangle_it5.995
r_dihedral_angle_1_deg5.868
r_scbond_it4.154
r_mcangle_it2.656
r_mcbond_it1.588
r_angle_refined_deg1.224
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.273
r_dihedral_angle_4_deg17.302
r_dihedral_angle_3_deg14.725
r_scangle_it5.995
r_dihedral_angle_1_deg5.868
r_scbond_it4.154
r_mcangle_it2.656
r_mcbond_it1.588
r_angle_refined_deg1.224
r_nbtor_refined0.307
r_nbd_refined0.199
r_symmetry_vdw_refined0.165
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.137
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5723
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction