2YVB | pdb_00002yvb

High resolution X-ray crystal structure of Tetragonal 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	PDB	193L	pdb entry 193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.7	293	0.04N NaOAc/HOAc buffer, pH 4.7, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.341	α = 90
b = 79.341	β = 90
c = 37.867	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	293	IMAGE PLATE	RIGAKU			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.62	55.9	98.6			15495	15495	1	1	23.872

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.62		98.6				15495

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 193L	1.62	28.1	1	1	15495	15495	789	98.55	0.23095	0.23095	0.22855	0.23	0.2773	0.28	RANDOM	23.872

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]
-0.39			-0.39		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.65
r_scangle_it	5.972
r_dihedral_angle_1_deg	4.989
r_scbond_it	3.999
r_mcangle_it	2.677
r_angle_refined_deg	2.593
r_mcbond_it	1.951
r_angle_other_deg	1.366
r_symmetry_hbond_refined	0.506
r_symmetry_vdw_other	0.493
r_symmetry_vdw_refined	0.453
r_nbd_refined	0.236
r_nbd_other	0.22
r_symmetry_hbond_other	0.207
r_xyhbond_nbd_refined	0.203
r_chiral_restr	0.168
r_bond_refined_d	0.03
r_gen_planes_refined	0.017
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
AUTOMAR	data reduction
AMoRE	phasing