5JML | pdb_00005jml

X-ray structure of the complex between bovine pancreatic ribonuclease and penthachlorocarbonyliridate(III) (2 months of soaking)

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 soium citrate pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.592	α = 90
b = 32.388	β = 89.97
c = 72.595	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		2015-06-16	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	2.29	72.59	96.5	0.139	1.72	2.4		10756

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	2.29	2.34	97.8		0.557	2	2.3

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	2.29	72.59	9837	490	96.01	0.22874	0.2255	0.23	0.2937	0.29	RANDOM	35.745

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]
-1.28		-1.32	-0.22		1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.008
r_dihedral_angle_3_deg	14.703
r_dihedral_angle_4_deg	12.924
r_dihedral_angle_1_deg	7.691
r_long_range_B_refined	6.914
r_long_range_B_other	6.695
r_mcangle_it	4.084
r_mcangle_other	4.068
r_scangle_other	3.928
r_mcbond_it	2.542
r_mcbond_other	2.536
r_angle_refined_deg	2.457
r_scbond_it	2.333
r_scbond_other	2.333
r_angle_other_deg	1.253
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.005
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	66
Heterogen Atoms	22

Software

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