1H6M

Covalent glycosyl-enzyme intermediate of hen egg white lysozyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		REFINED COORDINATES FOR APO STRUCTURE E35Q MUTANT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	289	CRYSTALS 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 coefficient	Solvent content
1.9	39.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.632	α = 90
b = 78.632	β = 90
c = 36.7	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RAXIS	OSMIC MIRRORS	2000-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.64	20	99.3	0.05	25	5.2		14536

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.7	96.3		0.19	4.6	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	REFINED COORDINATES FOR APO STRUCTURE E35Q MUTANT	1.64	18	13781	738	99.3	0.172	0.17	0.222	RANDOM

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
Key	Refinement Restraint Deviation
r_scangle_it	4.199
r_mcangle_it	2.822
r_scbond_it	2.663
r_mcbond_it	1.825
r_angle_other_deg	1.823
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.231
r_symmetry_vdw_refined	0.215
r_symmetry_hbond_refined	0.207
r_chiral_restr	0.135
r_metal_ion_refined	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing