7P4R | pdb_00007p4r

Ultra High Resolution X-ray Structure of Orthorhombic Bovine Pancreatic Ribonuclease at 100K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RN3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7	277	100mg of powdered Ribonuclease A in 1ml of distilled water dissolved in 2ml of ice cold absolute ethanol.

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.998	α = 90
b = 45.697	β = 90
c = 51.89	γ = 90

Symmetry
Space Group	P 21 21 21

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		2014-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.77	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	0.85	51.89	95.2	0.076	0.091	0.049	13.2	6.2		87934

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.85	0.86	65.2		0.697	0.893	0.55	3.8	3.8

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3rn3	0.85	34.294	85346	4279	92.225	0.113	0.1123	0.11	0.1291	0.13	7.596

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]
0.173			0.379		-0.551

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.722
r_dihedral_angle_3_deg	13.537
r_dihedral_angle_4_deg	8.337
r_dihedral_angle_1_deg	7.503
r_lrange_it	5.422
r_rigid_bond_restr	5.284
r_lrange_other	3.251
r_angle_refined_deg	2.474
r_scangle_it	1.726
r_angle_other_deg	1.68
r_scbond_it	1.582
r_scbond_other	1.45
r_scangle_other	1.348
r_mcangle_it	1.255
r_mcangle_other	1.254
r_mcbond_it	0.926
r_mcbond_other	0.922
r_symmetry_nbd_refined	0.383
r_symmetry_xyhbond_nbd_refined	0.352
r_nbd_other	0.344
r_xyhbond_nbd_refined	0.331
r_symmetry_xyhbond_nbd_other	0.301
r_nbd_refined	0.263
r_symmetry_nbd_other	0.222
r_nbtor_refined	0.189
r_chiral_restr	0.127
r_symmetry_nbtor_other	0.107
r_bond_refined_d	0.02
r_gen_planes_refined	0.017
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	951
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
xia2	data scaling
MOLREP	phasing