1R8O

Crystal structure of an unusual Kunitz-type trypsin inhibitor from Copaifera langsdorffii seeds

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.3	291	25% PEG4000 in 0.1M sodium acetate buffer, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.71	α = 90
b = 58.71	β = 90
c = 93.75	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2000-09-04	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2000-09-15	M	SINGLE WAVELENGTH
3	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2000-09-18	M	SINGLE WAVELENGTH
1,2,3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.54	LNLS	D03B-MX1
2	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.54	LNLS	D03B-MX1
3	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.54	LNLS	D03B-MX1

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
1,2,3	1.83	25.28	95.7	0.089	23.6	8.2	15027	14387			14.2

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)
1,2,3	1.83	1.87	97.6		0.508	3.3	5.4	14387

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIR QUICK CRIO-SOAKING METHOD	THROUGHOUT	1.83	25.28	15027	14387	703	95.7	0.17	0.17	0.16844	0.21237	RANDOM	13.229

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]
0.21			0.21		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.559
r_scangle_it	4.823
r_scbond_it	3.052
r_mcangle_it	1.885
r_angle_refined_deg	1.734
r_mcbond_it	1.064
r_symmetry_hbond_refined	0.464
r_symmetry_vdw_refined	0.396
r_xyhbond_nbd_refined	0.256
r_nbd_refined	0.229

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.559
r_scangle_it	4.823
r_scbond_it	3.052
r_mcangle_it	1.885
r_angle_refined_deg	1.734
r_mcbond_it	1.064
r_symmetry_hbond_refined	0.464
r_symmetry_vdw_refined	0.396
r_xyhbond_nbd_refined	0.256
r_nbd_refined	0.229
r_chiral_restr	0.134
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1267
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	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 R01GM133198.