9P5F | pdb_00009p5f

Crystal structure of hen egg white lysozyme at 100 Kelvin with Mineral Oil

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
1.99	38.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.431	α = 90
b = 78.431	β = 90
c = 37.126	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	1.498	25.496	99.687	0.99	18	1		19120

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	1.498	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	1.498	25.496	19120	943	99.687	0.175	0.1736	0.2016	0.2055	0.2336	9.345

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_6_deg	18.07
r_dihedral_angle_3_deg	13.192
r_dihedral_angle_2_deg	9.812
r_dihedral_angle_1_deg	6.458
r_lrange_it	5.6
r_lrange_other	5.323
r_scangle_it	2.897
r_scangle_other	2.895
r_scbond_it	2.111
r_scbond_other	2.109
r_angle_refined_deg	1.819
r_mcangle_other	1.36
r_mcangle_it	1.355
r_mcbond_it	0.895
r_mcbond_other	0.893
r_angle_other_deg	0.634
r_xyhbond_nbd_refined	0.309
r_nbd_refined	0.268
r_symmetry_xyhbond_nbd_refined	0.25
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.182
r_nbd_other	0.14
r_chiral_restr	0.096
r_symmetry_nbd_refined	0.087
r_symmetry_nbtor_other	0.077
r_metal_ion_refined	0.062
r_gen_planes_refined	0.011
r_bond_refined_d	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	132
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement