4RW1 | pdb_00004rw1

Hen egg-white lysozyme structure from a spent-beam experiment at LCLS: original beam

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ET8	PDB ENTRY 4ET8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	3	293	After crystallization, the solution used for growing the crystals (20 % NaCl, 6 % PEG 6000, 1 M Na acetate pH 3.0) was exchanged for storage solution (10 % NaCl, 1.0 M Na acetate pH 3.4), batch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.24	α = 90
b = 79.24	β = 90
c = 38.23	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	PIXEL	CSPAD	KB mirrors	2012-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.63	SLAC LCLS	CXI

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	1.9	40	100			10048	10048

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	1.9	2	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 4ET8	1.9	32.05	9531	9531	517	100	0.22085	0.22085	0.21895	0.22	0.25575	0.25	RANDOM, SAME AS FOR 4ET8	25.05

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]
-0.18			-0.18		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.052
r_dihedral_angle_4_deg	14.052
r_dihedral_angle_3_deg	13.166
r_dihedral_angle_1_deg	5.594
r_scangle_it	2.397
r_scbond_it	1.407
r_angle_refined_deg	1.023
r_angle_other_deg	0.905
r_mcangle_it	0.877
r_mcbond_it	0.435

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.052
r_dihedral_angle_4_deg	14.052
r_dihedral_angle_3_deg	13.166
r_dihedral_angle_1_deg	5.594
r_scangle_it	2.397
r_scbond_it	1.407
r_angle_refined_deg	1.023
r_angle_other_deg	0.905
r_mcangle_it	0.877
r_mcbond_it	0.435
r_mcbond_other	0.068
r_chiral_restr	0.061
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	2

Software

Software
Software Name	Purpose
LCLS	data collection
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
REFMAC	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.