9RUV | pdb_00009ruv

X-ray structure of the adduct formed upon reaction of dirhodium-tetraacetate with lysozyme at body temperature

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	310	2.0 M sodium formate, 0.1 M hepes buffer pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.43	α = 90
b = 80.43	β = 90
c = 36.14	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	310	PIXEL	DECTRIS PILATUS 6M		2024-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.12	56.873	94	0.092	0.998	13.2	11.4		6617

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.15	100		2.788	0.405	0.9	11.8

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	2.12	56.873	6515	332	91.4	0.201	0.1977	0.203	0.2612	0.2601	61.2

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]
-0.172			-0.172		0.344

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.665
r_dihedral_angle_4_deg	19.493
r_dihedral_angle_3_deg	17.175
r_lrange_it	10.548
r_lrange_other	10.444
r_scangle_it	9.512
r_scangle_other	8.783
r_dihedral_angle_1_deg	7.25
r_mcangle_it	6.348
r_mcangle_other	6.084
r_scbond_it	5.656
r_scbond_other	5.645
r_mcbond_it	4.561
r_mcbond_other	4.554
r_angle_refined_deg	1.571
r_angle_other_deg	1.355
r_nbd_refined	0.23
r_symmetry_nbd_other	0.202
r_symmetry_nbd_refined	0.191
r_nbd_other	0.188
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.166
r_ext_dist_refined_d	0.133
r_symmetry_xyhbond_nbd_refined	0.102
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_symmetry_xyhbond_nbd_other	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	8

Software

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