1IEE | pdb_00001iee

STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME AT 0.94 A FROM CRYSTALS GROWN BY THE COUNTER-DIFFUSION METHOD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LSA	PDB ENTRY 1LSA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Counter-Diffusion in modified APCF reactors	4.5	293	CRYSTALLISATION TOOK PLACE IN THE EUROPEAN SPACE AGENCY (ESA) ADVANCED PROTEIN CRYSTALLISATION FACILITY (APCF) ONBOARD THE NASA SPACE SHUTTLE'S STS-95 MISSION. A NEW APCF REACTOR WITH A LONG PROTEIN CHAMBER (67 MM) WAS DESIGNED TO PERFORM CRYSTALLIZATION USING THE COUNTER-DIFFUSION METHOD UNDER MICROGRAVITY CONDITIONS. THE PROTEIN CHAMBER WAS FILLED WITH A SOLUTION OF 99 MG/ML OF HEN EGG WHITE LYSOZYME (SUPPLIED BY SEIKAGAKU, BATCH NUMBER 100940, LOT E96302) DISSOLVED IN 0.05 M ACETATE BUFFER (PH 4.5). THE SALT CHAMBER CONTAINED 20% W/V NACL AND 0.05 M ACETATE BUFFER (PH 4.5). THE ROTATORY PLUG CONNECTING THE PROTEIN AND THE SALT CHAMBERS WAS FILLED WITH 10% W/V NACL, 0.5% W/V AGAROSE GEL AND 0.05 M ACETATE BUFFER. CRYSTALLISATION TOOK PLACE IN MICROGRAVITY AT 20+/-0.1 C., Counter-Diffusion in modified APCF reactors, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.67	26.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.061	α = 90
b = 77.061	β = 90
c = 37.223	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	110	IMAGE PLATE	MARRESEARCH		1998-12-10	M	SINGLE WAVELENGTH
2	1	110	IMAGE PLATE	MARRESEARCH		1998-12-10

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.8337	EMBL/DESY, HAMBURG	BW7B
2	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.9057	EMBL/DESY, HAMBURG	X11

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	0.94	31	98.9	0.052	15.5	5.5	402070	72390		-3	8.7

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)
	0.94	0.96	88.6		0.329	2.6		3912

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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 1LSA	0.94	31	-3	72390	72390	3655	98.9	0.1226	0.1226	0.1233	0.13	0.1509	0.14	RANDOM	14.4

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
37	956.3	1173.6

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.115
s_zero_chiral_vol	0.104
s_approx_iso_adps	0.072
s_anti_bump_dis_restr	0.067
s_similar_adp_cmpnt	0.048
s_angle_d	0.037
s_from_restr_planes	0.031
s_bond_d	0.016
s_rigid_bond_adp_cmpnt	0.006
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1229
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.