5OBE | pdb_00005obe

X-ray structure of the adduct formed upon reaction of ribonuclease A with the compound fac-[RuII(CO)3Cl2(N3-MBI), MBI=methyl-benzimidazole

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	22% PEG4K, 10 mM sodium citrate pH 5.1 Soaking: 3 days Ligand con-centration: 5 mM

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.651	α = 90
b = 32.983	β = 90.21
c = 73.046	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	CCD	RIGAKU SATURN 944	mirrors	2014-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.82	73.05	97.6	0.072	6.3	2.4		21285

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.85	95.4		0.384	1.7	1.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1JVT mol A	1.82	73.05	20184	1091	95.14	0.16896	0.16546	0.17	0.23577	0.24	RANDOM	30.82

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]
-0.48		-0.52	-0.11		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.322
r_dihedral_angle_3_deg	14.687
r_dihedral_angle_4_deg	14.169
r_long_range_B_refined	8.766
r_long_range_B_other	8.451
r_dihedral_angle_1_deg	7.266
r_mcangle_it	4.214
r_mcangle_other	4.213
r_scangle_other	4.098
r_scbond_it	2.848
r_mcbond_it	2.771
r_mcbond_other	2.766
r_scbond_other	2.661
r_angle_refined_deg	1.771
r_angle_other_deg	1.016
r_chiral_restr	0.113
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1902
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing