9P5B | pdb_00009p5b

Crystal structure of hen egg white lysozyme at 100 Kelvin with Lard

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 sodium chloride, 100 mM sodium acetate, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2	38.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.448	α = 90
b = 78.448	β = 90
c = 37.228	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	PIXEL	Bruker PHOTON II		2024-07-01	M	SINGLE WAVELENGTH

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	1.499	24.807	99	0.99	19	1		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	1.499	10			0.99

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.499	24.807	19148	943	99.719	0.217	0.2158	0.2253	0.247	0.2495	11.397

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]
-0.011			-0.011		0.022

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.783
r_dihedral_angle_3_deg	11.515
r_dihedral_angle_2_deg	8.673
r_dihedral_angle_1_deg	6.64
r_lrange_other	4.194
r_lrange_it	4.186
r_scangle_it	3.329
r_scangle_other	3.327
r_scbond_it	2.125
r_scbond_other	2.123
r_angle_refined_deg	1.845
r_mcangle_other	1.781
r_mcangle_it	1.777
r_mcbond_it	1.146
r_mcbond_other	1.139
r_angle_other_deg	0.643
r_xyhbond_nbd_refined	0.422
r_nbd_refined	0.263
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.184
r_nbd_other	0.144
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.077
r_metal_ion_refined	0.073
r_symmetry_nbd_refined	0.062
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_symmetry_xyhbond_nbd_refined	0.009
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	89
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement