7BEB

Unusual structural features in the adduct of dirhodium tetraacetate with lysozyme (4)

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	4.5	293	0.1 M sodium acetate, 20% ethylene glicol, 0.6 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.604	α = 90
b = 78.604	β = 90
c = 37.307	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-F		2020-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.32	55.58	95.4	0.047	0.013	1	28.8	25.8		26513

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	1.32	1.37	51.1		2.55	0.72	0.612		25.9

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	1.32	55.58	26513	1286	95.384	0.18	0.1777	0.2233	27.339

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_2_deg	34.632
r_dihedral_angle_4_deg	19.989
r_dihedral_angle_3_deg	12.66
r_lrange_it	7.461
r_lrange_other	7.329
r_dihedral_angle_1_deg	6.438
r_scangle_it	5.514
r_scangle_other	5.511
r_scbond_it	3.704
r_scbond_other	3.704
r_mcangle_other	2.672
r_mcangle_it	2.66
r_angle_refined_deg	2.394
r_mcbond_it	2.324
r_mcbond_other	1.978
r_angle_other_deg	1.643
r_nbd_refined	0.252
r_nbd_other	0.248
r_ext_dist_refined_d	0.247
r_symmetry_xyhbond_nbd_refined	0.242
r_xyhbond_nbd_refined	0.221
r_symmetry_nbd_other	0.214
r_xyhbond_nbd_other	0.201
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.156
r_symmetry_xyhbond_nbd_other	0.136
r_metal_ion_refined	0.104
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.009
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	96

Software

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