X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AKR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529518% PEG 4000, 0.2 M ammonium citrate, 2% butanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3948.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.941α = 90
b = 96.224β = 106.23
c = 77.926γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0ALS8.2.1

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
11.954097.90.0617.92.7611205981626
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)
11.952.0297.80.4492.322.75934

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 REPLACEMENTTHROUGHOUT2AKR1.9527.915929558076121997.510.20.20.1990.245RANDOM32.361
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]
-0.01-0.03-0.040.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.008
r_dihedral_angle_4_deg17.047
r_dihedral_angle_3_deg13.811
r_dihedral_angle_1_deg4.985
r_scangle_it3.377
r_scbond_it2.301
r_angle_refined_deg1.708
r_mcangle_it1.478
r_mcbond_it0.997
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.008
r_dihedral_angle_4_deg17.047
r_dihedral_angle_3_deg13.811
r_dihedral_angle_1_deg4.985
r_scangle_it3.377
r_scbond_it2.301
r_angle_refined_deg1.708
r_mcangle_it1.478
r_mcbond_it0.997
r_nbtor_refined0.31
r_nbd_refined0.209
r_xyhbond_nbd_refined0.209
r_symmetry_vdw_refined0.182
r_symmetry_hbond_refined0.15
r_chiral_restr0.123
r_bond_refined_d0.015
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5950
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms288

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing