5ARL

crystal structure of porcine RNase 4 D80A mutant in complex with dCMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ARJ	PDB ENTRY 5ARJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		0.1 M SODIUM CITRATE PH 5.6, 20 % (V/V) 2-PROPANOL, 20 % (W/V) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.962	α = 89.78
b = 62.515	β = 79.21
c = 70.216	γ = 78.9

Symmetry
Space Group	P 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		2014-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	2.6	29.5	91.5	0.1	27	3.1		14168		6

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	2.6	2.72	65.6		0.41	10.7	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	PDB ENTRY 5ARJ	2.61	68.94	13322	723	90.78	0.25486	0.25232	0.26	0.29958	0.3	RANDOM	46.109

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]
-2.89	-2.15	-2.18	0.48	4	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.156
r_dihedral_angle_3_deg	15.541
r_dihedral_angle_4_deg	13.32
r_dihedral_angle_1_deg	7.082
r_mcangle_it	5.823
r_scbond_it	4.116
r_mcbond_it	3.669
r_mcbond_other	3.669
r_angle_refined_deg	1.514
r_angle_other_deg	1.136
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.006
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3864
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing