2QCA | pdb_00002qca

A New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	295	Reservoir: 0.6 ml of 30% PEG 3350 in 0.1 M HEPES at pH 7.0. Sample: 2 ul 10-40 mg/ml Protein in 0.1 M HEPES at pH 7.0 and 2 ul of 0.1 M DGP, cholesterol, thymine and oxamic acid in 15% PEG 3350 and 9.1 M HEPES at pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.08	α = 90
b = 55.08	β = 90
c = 39.2	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	IMAGE PLATE	RIGAKU RAXIS	OSMIC MIRRORS	2006-01-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	1.33	27.54	89.3	0.049	13.7	3.33		27155			27.06

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	1.33	1.38	24.9		0.491	0.8	1.49

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FREE R	PDB ENTRY 1RNO	1.33	27.54	26810	2672	79.4	0.1253	0.1253	0.1194	0.12	0.1771	0.17	RANDOM	39.6

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
12	914	1105.57

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.091
s_non_zero_chiral_vol	0.073
s_similar_adp_cmpnt	0.067
s_zero_chiral_vol	0.065
s_angle_d	0.032
s_from_restr_planes	0.03
s_anti_bump_dis_restr	0.02
s_bond_d	0.012
s_rigid_bond_adp_cmpnt	0.004
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	951
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	46

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.