2RBN

N-phenylglycinonitrile in complex with T4 lysozyme L99A/M102Q


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LGU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12772.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7555.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.131α = 90
b = 60.131β = 90
c = 96.886γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)2006-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.979462SSRLBL9-1

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
11.2952.0698.80.08106.65113651136
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)
1.291.341000.56975120

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 DIFFRACTIONTHROUGHOUT1LGU1.2952.065107451074260098.760.1790.1790.1780.191RANDOM14.879
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]
0.040.020.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.496
r_dihedral_angle_4_deg13.18
r_dihedral_angle_3_deg11.153
r_dihedral_angle_1_deg4.768
r_scangle_it2.479
r_sphericity_free2.393
r_scbond_it2.388
r_rigid_bond_restr2.312
r_sphericity_bonded2.057
r_angle_refined_deg1.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.496
r_dihedral_angle_4_deg13.18
r_dihedral_angle_3_deg11.153
r_dihedral_angle_1_deg4.768
r_scangle_it2.479
r_sphericity_free2.393
r_scbond_it2.388
r_rigid_bond_restr2.312
r_sphericity_bonded2.057
r_angle_refined_deg1.071
r_mcangle_it1.007
r_mcbond_it0.806
r_nbtor_refined0.307
r_nbd_refined0.192
r_symmetry_vdw_refined0.153
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.112
r_chiral_restr0.071
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1329
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms15

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACphasing