9P69 | pdb_00009p69

Crystal structure of hen egg white lysozyme at 300 Kelvin with Vaseline (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
2.09	41.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.891	α = 90
b = 78.891	β = 90
c = 38.526	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	300	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	1.497	26.019	99	0.99	18	1		19892

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	1.497	26.019	19892	973	98.583	0.184	0.1825	0.1826	0.2084	0.2069	18.605

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]
-0.002			-0.002		0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.339
r_dihedral_angle_3_deg	11.595
r_dihedral_angle_2_deg	10.818
r_lrange_it	6.941
r_lrange_other	6.939
r_dihedral_angle_1_deg	6.585
r_scangle_it	5.77
r_scangle_other	5.766
r_scbond_it	3.691
r_scbond_other	3.688
r_mcangle_other	2.678
r_mcangle_it	2.667
r_angle_refined_deg	2.01
r_mcbond_it	1.792
r_mcbond_other	1.788
r_angle_other_deg	0.713
r_xyhbond_nbd_refined	0.477
r_nbd_refined	0.257
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.182
r_chiral_restr	0.12
r_nbd_other	0.119
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_refined	0.055
r_metal_ion_refined	0.035
r_bond_refined_d	0.011
r_gen_planes_refined	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	51
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement