2EPE | pdb_00002epe

Crystal structure analysis of Hen egg white lysozyme grown by capillary method

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	capillary method	4.7	298	0.04m NAOAC/HOAC buffer, pH 4.7, capillary method, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.243	α = 90
b = 79.243	β = 90
c = 37.829	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 RU200

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	2.5	39.53					4332	1	1	22.02

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)
	2.5	39.53	98.5		0.092	5.9		4332

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 (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	2.5	39.53	4189	203	98.5	0.16681	0.16454	0.17	0.21131	0.21	RANDOM	22.024

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]
0.05			0.05		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.007
r_scangle_it	7.435
r_scbond_it	4.907
r_dihedral_angle_1_deg	4.459
r_mcangle_it	3.235
r_angle_refined_deg	2.441
r_angle_other_deg	1.964
r_mcbond_it	1.939
r_symmetry_hbond_refined	1.304
r_symmetry_hbond_other	0.575
r_symmetry_vdw_refined	0.427
r_symmetry_vdw_other	0.384
r_xyhbond_nbd_other	0.248
r_nbd_refined	0.24
r_nbd_other	0.22
r_chiral_restr	0.175
r_xyhbond_nbd_refined	0.142
r_bond_refined_d	0.037
r_gen_planes_refined	0.017
r_gen_planes_other	0.013
r_bond_other_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms

Software

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