5OBD | pdb_00005obd

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

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 cit-rate pH 5.1 Soaking: 14 days Ligand concentration: 5 mM

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.628	α = 90
b = 32.773	β = 90
c = 72.246	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	2014-05-28	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	1.98	72.25	92.2	0.103	8.2	2.3		15576

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	1.98	2.1	81.9		0.448	2.2	1.7

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	1.98	72.25	14790	785	91.27	0.18142	0.17641	0.18	0.27936	0.28	RANDOM	30.535

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]
-1.2		0.78	-0.87		2.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.328
r_dihedral_angle_3_deg	15.006
r_dihedral_angle_4_deg	13.652
r_long_range_B_refined	7.577
r_long_range_B_other	7.206
r_dihedral_angle_1_deg	6.801
r_mcangle_it	4.02
r_mcangle_other	4.019
r_scangle_other	3.531
r_mcbond_it	2.488
r_mcbond_other	2.488
r_scbond_it	2.302
r_scbond_other	2.232
r_angle_refined_deg	1.626
r_angle_other_deg	1.132
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
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	393
Heterogen Atoms	23

Software

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