1H6M

Covalent glycosyl-enzyme intermediate of hen egg white lysozyme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherREFINED COORDINATES FOR APO STRUCTURE E35Q MUTANT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.8289CRYSTALS OF THE HEWL COVALENT INTERMEDIATE WERE GROWN BY THE HANGING-DROPLET VAPOUR DIFFUSION METHOD OVER 4 DAYS AT 16 C. THE DROPLET CONTAINED 2.5 UL OF A SOLUTION OF 7.5 MG/ML HEWL(E35Q), 20 MM NAG2FGLCF, 200 MM SODIUM ACETATE (NAOAC) BUFFER PH 5.0 AND 2.5 UL OF RESERVOIR SOLUTION (200MM) NAOAC, CONTAINING 4.0 % NACL (W/V), PH 4.5 WAS SUSPENDED OVER THE RESERVOIR SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
1.939.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.632α = 90
b = 78.632β = 90
c = 36.7γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERAXISOSMIC MIRRORS2000-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.642099.30.05255.214536
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)
11.641.796.30.194.62.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTREFINED COORDINATES FOR APO STRUCTURE E35Q MUTANT1.64181378173899.30.1720.170.170.222RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.199
r_mcangle_it2.822
r_scbond_it2.663
r_mcbond_it1.825
r_angle_other_deg1.823
r_nbd_refined0.237
r_xyhbond_nbd_refined0.231
r_symmetry_vdw_refined0.215
r_symmetry_hbond_refined0.207
r_chiral_restr0.135
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing