1N6Y | pdb_00001n6y

RIP-phasing on Bovine Trypsin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	25% polyethylene glycol (PEG) 8000, 0.2 M ammonium sulphate, 0.1 M Tris buffer, pH 8, and 100 mM benzylamine, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.241	α = 90
b = 56.752	β = 90
c = 66.204	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	CCD	ADSC QUANTUM 4		2001-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9763	ESRF	ID14-4

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	1.4	42	99.83	0.05	11.2	13.1	41043	40971		-3	12.31

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	1.4	1.47	97.4		0.312	2.7	11.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	RIP - Radiation-Damage Induced Phasing	THROUGHOUT	1.4	42	40971	40971	2061	99.83	0.142	0.142	0.14051	0.17021	RANDOM	14.552

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]
-0.1			0.02		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	7.18
r_dihedral_angle_1_deg	6.285
r_scangle_it	4.876
r_scbond_it	3.656
r_mcangle_it	2.799
r_sphericity_free	1.774
r_mcbond_it	1.758
r_angle_refined_deg	1.633
r_rigid_bond_restr	1.419
r_nbd_refined	0.199

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	7.18
r_dihedral_angle_1_deg	6.285
r_scangle_it	4.876
r_scbond_it	3.656
r_mcangle_it	2.799
r_sphericity_free	1.774
r_mcbond_it	1.758
r_angle_refined_deg	1.633
r_rigid_bond_restr	1.419
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.156
r_chiral_restr	0.125
r_xyhbond_nbd_refined	0.125
r_bond_refined_d	0.017
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1629
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	25

Software

Software
Software Name	Purpose
ProDC	data collection
SCALA	data scaling
SHELXD	phasing
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

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.