7BEC

Unusual structural features in the adduct of dirhodium tetraacetate with lysozyme (5)

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, 0.1 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.7	α = 90
b = 78.7	β = 90
c = 37.245	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	1.74	35.19	91.1	0.07	0.02	1	24.7	25		11349

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	1.74	1.83	36		3.12	0.848	0.474	1.1	27.6

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	1.74	35.19	11349	555	90.756	0.187	0.1847	0.2284	42.938

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]
-0.227			-0.227		0.455

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.207
r_dihedral_angle_4_deg	18.595
r_dihedral_angle_3_deg	14.871
r_lrange_other	9.528
r_lrange_it	9.527
r_dihedral_angle_1_deg	7.122
r_scangle_it	7.037
r_scangle_other	7.032
r_scbond_it	4.462
r_scbond_other	4.459
r_mcangle_other	3.977
r_mcangle_it	3.969
r_mcbond_it	3.025
r_mcbond_other	3.006
r_angle_refined_deg	1.553
r_angle_other_deg	1.384
r_xyhbond_nbd_refined	0.228
r_nbd_refined	0.222
r_nbd_other	0.194
r_symmetry_nbd_other	0.191
r_ext_dist_refined_d	0.19
r_symmetry_xyhbond_nbd_refined	0.171
r_symmetry_nbd_refined	0.166
r_nbtor_refined	0.159
r_metal_ion_refined	0.093
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.079
r_xyhbond_nbd_other	0.025
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
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	75
Heterogen Atoms	36

Software

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