9RBT | pdb_00009rbt

X-ray structure of decavanadate/lysozyme adduct obtained when the protein is treated with Cs2[V(V)2O4(mal)2]2H2O (structure B)

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	293	1.1 M sodium chloride, 0.1 M sodium acetate pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.01	α = 90
b = 80.01	β = 90
c = 36.27	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		2024-10-14	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)	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	1.18	40.01	89.1	0.999	19.4	20		35010

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.18	1.2			0.371

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	1.18	40.01	28531	1341	72.622	0.193	0.1914	0.2	0.2347	0.2396	25.367

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]
-0.564			-0.564		1.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.245
r_dihedral_angle_4_deg	22.207
r_dihedral_angle_3_deg	14.271
r_scangle_it	7.236
r_dihedral_angle_1_deg	7.197
r_lrange_it	6.124
r_scangle_other	6.107
r_scbond_it	5.811
r_lrange_other	5.489
r_rigid_bond_restr	5.264
r_scbond_other	5.003
r_mcangle_other	4.14
r_mcangle_it	4.139
r_mcbond_it	3.499
r_mcbond_other	3.48
r_angle_refined_deg	2.414
r_angle_other_deg	1.642
r_symmetry_nbd_refined	0.29
r_nbd_refined	0.249
r_symmetry_nbd_other	0.2
r_xyhbond_nbd_refined	0.18
r_nbd_other	0.174
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.16
r_chiral_restr	0.103
r_metal_ion_refined	0.085
r_symmetry_nbtor_other	0.084
r_symmetry_metal_ion_refined	0.044
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	45

Software

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