2E3W

X-ray structure of native RNase A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IZP	PDB entry 1IZP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.89	292	Well solution: Combination of Hampton Index Reagents 3 and 9, Final solution: 0.1 M Bis-tris, 1.0 M ammonium sulfate, 1.5 M NaCl, pH 5.89, Drop: 2 microliter well solution + 2 microliter 10 mg/ml protein solution in water, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.167	α = 90
b = 64.167	β = 90
c = 63.626	γ = 120

Symmetry
Space Group	P 32 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	77	CCD	MARMOSAIC 300 mm CCD		2006-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.90020	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.05	50					69871

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1IZP	1.05	20	66348	3523	98.58	0.19329	0.1925	0.20783	RANDOM	15.424

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]
-0.33	-0.17		-0.33		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.465
r_dihedral_angle_4_deg	19.959
r_dihedral_angle_3_deg	11.869
r_sphericity_bonded	6.785
r_dihedral_angle_1_deg	6.333
r_scangle_it	3.53
r_scbond_it	2.719
r_mcangle_it	2.507
r_rigid_bond_restr	1.833
r_mcbond_it	1.804
r_angle_refined_deg	1.57
r_nbtor_refined	0.298
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.211
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.156
r_chiral_restr	0.106
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	984
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement