9P5W | pdb_00009p5w

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

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	38.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.488	α = 90
b = 78.488	β = 90
c = 37.169	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	21.769	99	0.99	18	1		19152

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	21.769			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	21.769	19152	945	99.823	0.169	0.1674	0.1765	0.1975	0.2063	9.851

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	23.175
r_dihedral_angle_6_deg	17.846
r_dihedral_angle_3_deg	13.209
r_dihedral_angle_1_deg	6.452
r_lrange_it	4.863
r_lrange_other	4.56
r_scangle_it	3.175
r_scangle_other	3.173
r_scbond_it	2.438
r_scbond_other	2.436
r_angle_refined_deg	1.843
r_mcangle_other	1.444
r_mcangle_it	1.443
r_mcbond_it	0.955
r_mcbond_other	0.954
r_angle_other_deg	0.631
r_xyhbond_nbd_refined	0.295
r_nbd_refined	0.265
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.182
r_nbd_other	0.161
r_symmetry_xyhbond_nbd_refined	0.132
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.081
r_metal_ion_refined	0.068
r_symmetry_nbd_refined	0.017
r_bond_refined_d	0.011
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	178
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement