8D62 | pdb_00008d62

Crystal structure of hen egg white lysozyme at 150 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	38.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.72	α = 90
b = 78.72	β = 90
c = 37.078	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	150	CMOS	BRUKER PHOTON 100		2020-10-13	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	24.91	99.85	0.789	7.19	1.91		19259

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	24.91			0.789

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	24.906	19259	986	99.855	0.166	0.1645	0.17	0.19	0.2	10.019

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		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.512
r_dihedral_angle_4_deg	18.276
r_dihedral_angle_3_deg	11.681
r_dihedral_angle_1_deg	6.63
r_lrange_it	4.107
r_lrange_other	3.963
r_scangle_it	3.048
r_scangle_other	3.046
r_scbond_other	2.061
r_scbond_it	2.06
r_angle_refined_deg	1.83
r_angle_other_deg	1.617
r_mcangle_other	1.364
r_mcangle_it	1.363
r_mcbond_it	0.877
r_mcbond_other	0.858
r_symmetry_nbd_refined	0.275
r_nbd_refined	0.242
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.197
r_nbd_other	0.196
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.085
r_metal_ion_refined	0.066
r_xyhbond_nbd_other	0.042
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
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	126
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction