7P8R | pdb_00007p8r

X-ray structure of the adduct of a vanadium picolinate complex with RNase A at pH 5.1

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% PEG 4K 10 mM sodium citrate pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.23	α = 90
b = 33.02	β = 90.161
c = 72.71	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		2021-05-22	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	1.268	72.71	91.3	0.095	0.105	0.042	0.992	8.6	5		58090

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	1.268	1.29	79.8		0.664	0.761	0.365	0.828	2.1	4.2

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	1.27	72.71	57790	2754	91.291	0.161	0.158	0.16	0.2222	0.22	20.638

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]
-1.101		-0.021	0.651		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.638
r_dihedral_angle_3_deg	13.551
r_dihedral_angle_4_deg	13.521
r_dihedral_angle_1_deg	6.79
r_lrange_it	5.549
r_lrange_other	5.285
r_scangle_it	5.052
r_scangle_other	4.95
r_scbond_it	4.49
r_scbond_other	4.446
r_mcangle_it	4.143
r_mcangle_other	4.142
r_rigid_bond_restr	4.077
r_mcbond_it	3.66
r_mcbond_other	3.656
r_angle_refined_deg	3.549
r_angle_other_deg	1.621
r_nbd_other	0.238
r_nbd_refined	0.206
r_symmetry_nbd_other	0.2
r_symmetry_nbd_refined	0.2
r_xyhbond_nbd_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.192
r_xyhbond_nbd_other	0.181
r_nbtor_refined	0.168
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1862
Nucleic Acid Atoms
Solvent Atoms	389
Heterogen Atoms	30

Software

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