7QWH | pdb_00007qwh

X-ray structure of the adduct formed upon reaction of a vanadium hydroxyquinoline complex with RNase A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JVT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.1	293	22% PEG4K, 10 mM sodium citrate buffer pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.74	α = 90
b = 32.47	β = 90.511
c = 72.86	γ = 90

Symmetry
Space Group	C 1 2 1

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		2021-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.96	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.573	50.368	99	0.04	0.044	0.018	0.999	21.6	6		33104

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.573	1.6	92.9		0.725	0.826	0.384	0.645	2.2	4.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1jvt	1.573	50.368	33104	1553	98.951	0.176	0.1742	0.18	0.2223	0.23	30.521

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]
-0.055		0.122	0.03		0.023

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.035
r_dihedral_angle_3_deg	15.55
r_dihedral_angle_4_deg	12.976
r_lrange_it	7.357
r_lrange_other	7.23
r_dihedral_angle_1_deg	7.051
r_scangle_other	5.226
r_scangle_it	5.215
r_mcangle_other	4.294
r_mcangle_it	4.293
r_scbond_it	3.368
r_scbond_other	3.367
r_mcbond_it	2.872
r_mcbond_other	2.866
r_angle_refined_deg	1.736
r_angle_other_deg	1.508
r_nbd_other	0.218
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.184
r_symmetry_nbd_other	0.183
r_symmetry_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.165
r_symmetry_xyhbond_nbd_other	0.134
r_symmetry_nbd_refined	0.127
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1902
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	14

Software

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