8D8E | pdb_00008d8e

Crystal structure of hen egg white lysozyme at 300 Kelvin (Triplicate)

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
2.08	40.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.495	α = 90
b = 79.495	β = 90
c = 37.767	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	300	CMOS	BRUKER PHOTON 100		2020-11-24	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	56.21	99.58	0.806	8.77	1.9		20015

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	56.21			0.806

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3A8Z	1.5	56.21	20015	1032	99.582	0.176	0.1746	0.18	0.1959	0.21	22.015

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]
0.001			0.001		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.046
r_dihedral_angle_4_deg	17.936
r_dihedral_angle_3_deg	13.298
r_lrange_it	7.485
r_lrange_other	7.484
r_dihedral_angle_1_deg	6.645
r_scangle_it	6.077
r_scangle_other	6.073
r_scbond_it	3.923
r_scbond_other	3.919
r_mcangle_it	2.912
r_mcangle_other	2.912
r_mcbond_it	1.971
r_mcbond_other	1.938
r_angle_refined_deg	1.829
r_angle_other_deg	1.615
r_nbd_refined	0.235
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.118
r_nbd_other	0.117
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.105
r_metal_ion_refined	0.094
r_symmetry_nbtor_other	0.089
r_symmetry_nbd_refined	0.02
r_bond_refined_d	0.013
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	42
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction