8D5T | pdb_00008d5t

Crystal structure of hen egg white lysozyme at 100 Kelvin (Duplicate)

X-RAY DIFFRACTION

---

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	38.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.629	α = 90
b = 78.629	β = 90
c = 37.07	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	24.88	99.92	0.772	6.67	1.91		19148

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	24.88			0.772	6.67

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	24.877	19148	983	99.917	0.177	0.1755	0.18	0.2117	0.22	11.4

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]
0.012			0.012		-0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.598
r_dihedral_angle_4_deg	16.922
r_dihedral_angle_3_deg	12.517
r_dihedral_angle_1_deg	6.718
r_lrange_it	4.043
r_lrange_other	3.954
r_scangle_it	3
r_scangle_other	2.999
r_scbond_it	2.059
r_scbond_other	2.058
r_angle_refined_deg	1.795
r_angle_other_deg	1.615
r_mcangle_other	1.553
r_mcangle_it	1.551
r_mcbond_it	1.048
r_mcbond_other	0.977
r_nbd_refined	0.252
r_symmetry_nbd_other	0.198
r_symmetry_xyhbond_nbd_refined	0.18
r_nbd_other	0.177
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.084
r_symmetry_nbd_refined	0.065
r_metal_ion_refined	0.054
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
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	120
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction