8D5S

Crystal structure of hen egg white lysozyme at 100 Kelvin

X-RAY DIFFRACTION

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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
2.02	39.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.835	α = 90
b = 78.835	β = 90
c = 37.241	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	100	CMOS	BRUKER PHOTON 100		2020-10-05	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	25.62	99.68	0.778	6.15	1.9		19440

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	25.62			0.778	6.15

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	25.616	19440	994	99.682	0.181	0.1798	0.2128	11.868

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]
-0.003			-0.003		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.613
r_dihedral_angle_4_deg	20.226
r_dihedral_angle_3_deg	13.017
r_dihedral_angle_1_deg	6.865
r_lrange_it	4.272
r_lrange_other	4.209
r_scangle_it	3.097
r_scangle_other	3.095
r_scbond_it	2.129
r_scbond_other	2.127
r_angle_refined_deg	1.87
r_mcangle_it	1.676
r_mcangle_other	1.675
r_angle_other_deg	1.605
r_mcbond_it	1.157
r_mcbond_other	1.107
r_nbd_refined	0.249
r_symmetry_nbd_other	0.2
r_symmetry_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.171
r_nbd_other	0.166
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.093
r_symmetry_nbd_refined	0.09
r_symmetry_nbtor_other	0.087
r_metal_ion_refined	0.084
r_xyhbond_nbd_other	0.044
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction