7BE2

X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (6)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.01 M HEPES, 2.00 M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.93	α = 90
b = 78.93	β = 90
c = 37.12	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	DECTRIS PILATUS 6M		2020-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.5406	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.65	55.812	94	0.12	0.025	1	22.5	24.5		11800

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.8	52.6		3.23	0.68	0.51	1.3	22.4

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	193L	1.65	55.81	11800	595	80.601	0.185	0.1819	0.2341	30.659

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]
-0.023			-0.023		0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.069
r_dihedral_angle_4_deg	23.303
r_dihedral_angle_3_deg	14.523
r_lrange_it	8.384
r_lrange_other	8.349
r_dihedral_angle_1_deg	7.409
r_scangle_it	5.727
r_scangle_other	5.723
r_mcangle_it	3.551
r_mcangle_other	3.551
r_scbond_it	3.522
r_scbond_other	3.52
r_mcbond_it	2.475
r_mcbond_other	2.456
r_angle_refined_deg	1.546
r_angle_other_deg	1.411
r_nbd_refined	0.218
r_symmetry_xyhbond_nbd_refined	0.201
r_nbd_other	0.199
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.162
r_metal_ion_refined	0.147
r_symmetry_nbd_refined	0.112
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
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	106
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
MOSFLM	data scaling
PHASER	phasing