8D8A

Crystal structure of hen egg white lysozyme at 275 Kelvin (Duplicate)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A8Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	295	1.2 M NaCl and 100 mM AcONa pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.723	α = 90
b = 79.723	β = 90
c = 37.427	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	275	CMOS	BRUKER PHOTON 100		2020-11-04	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER TURBO X-RAY SOURCE	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.5	22.53	93.86	0.683	8.03	1.86		19138

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	22.53			0.683

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3A8Z	1.5	22.526	19138	973	93.86	0.232	0.2301	0.2597	21.402

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]
-0.009			-0.009		0.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.215
r_dihedral_angle_4_deg	22.774
r_dihedral_angle_3_deg	14.562
r_dihedral_angle_1_deg	7.041
r_lrange_it	5.605
r_lrange_other	5.604
r_scangle_it	4.479
r_scangle_other	4.476
r_scbond_it	2.985
r_scbond_other	2.983
r_mcangle_other	2.591
r_mcangle_it	2.589
r_mcbond_it	1.947
r_mcbond_other	1.936
r_angle_refined_deg	1.861
r_angle_other_deg	1.485
r_metal_ion_refined	0.26
r_nbd_other	0.235
r_nbd_refined	0.232
r_symmetry_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.195
r_symmetry_nbd_refined	0.193
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
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	43
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction