1PYL

Crystal structure of Ribonuclease Sa2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RGG	PDB ENTRY 1RGG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	ammonium sulfate, phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.98	α = 90
b = 34.13	β = 109.5
c = 72.27	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	298	IMAGE PLATE	RIGAKU	MIRRORS	1997-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	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	1.5	25	98.6	0.063	22.3	3.5	30643	30643			24.4

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)
	1.5	1.55	90.2		0.272	2.65		1894

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1RGG	1.507	25	29668	975	98.14	0.15	0.15009	0.14933	0.1723	RANDOM	22.179

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]
-0.55		-0.44	0.9		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	10.982
r_dihedral_angle_1_deg	6.464
r_scangle_it	5.178
r_sphericity_bonded	4.639
r_scbond_it	3.507
r_mcangle_it	2.653
r_angle_other_deg	1.745
r_mcbond_it	1.613
r_rigid_bond_restr	1.58
r_angle_refined_deg	1.54
r_nbd_refined	0.299
r_symmetry_vdw_other	0.259
r_nbd_other	0.257
r_xyhbond_nbd_refined	0.203
r_symmetry_vdw_refined	0.19
r_symmetry_hbond_refined	0.153
r_nbtor_other	0.134
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3024
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing