8PX0 | pdb_00008px0

Structure of ribonuclease A, solved at wavelength 2.75 A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20 mM sodium citrate pH 5.5, 28 % PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.98	α = 90
b = 32.62	β = 90.16
c = 72.49	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	80	PIXEL	DECTRIS PILATUS 12M		2019-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	2.7552	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.8	50.01	81.29	0.09291	0.09543	0.02108	0.995	24.67	17.5		17977

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.864	65.04		0.3414	0.3644	0.12	0.915	5.03	8.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.8	50.01	17074	903	81.34	0.20252	0.20063	0.21	0.23851	0.24	RANDOM	33.321

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]
-1.05		0.28	1.7		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.021
r_dihedral_angle_1_deg	6.888
r_long_range_B_other	6.246
r_long_range_B_refined	6.244
r_dihedral_angle_2_deg	5.848
r_scangle_other	4.444
r_mcangle_it	3.183
r_mcangle_other	3.182
r_scbond_it	3.012
r_scbond_other	3.011
r_mcbond_it	2.122
r_mcbond_other	2.119
r_angle_refined_deg	1.42
r_angle_other_deg	0.467
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	1875
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
HKL2Map	phasing