4ZOT | pdb_00004zot

Crystal structure of BbKI, a disulfide-free plasma kallikrein inhibitor at 1.4 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GO2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	rBbKI in 0.05 M Tris/HCl, pH 8.0, and 0.15 M NaCl was concentrated to 6.3 mg/ml and crystallized using the conditions 8% PEG 4000, 0.1 M sodium acetate, pH 4.6. Cryoprotectant solution - mother liquor with extra 25% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.736	α = 90
b = 59.462	β = 90
c = 64.011	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	MARMOSAIC 300 mm CCD	Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2013-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.4	50	96.1	0.048	0.048	0.054	0.024	10.2	5		34445		-3	16.2

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	1.4	1.42	93.3		0.628	0.704	0.311	0.752	1.9	4.8	1631

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 (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	THROUGHOUT	2GO2	1.4	43.57	32686	1726	96.06	0.1247	0.1226	0.12	0.1665	0.17	RANDOM	23.091

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]
-0.44			0.11		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.022
r_sphericity_free	29.752
r_dihedral_angle_4_deg	23.965
r_sphericity_bonded	16.485
r_dihedral_angle_3_deg	11.197
r_dihedral_angle_1_deg	7.645
r_mcangle_it	3.656
r_mcbond_it	2.943
r_mcbond_other	2.941
r_rigid_bond_restr	2.817

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.022
r_sphericity_free	29.752
r_dihedral_angle_4_deg	23.965
r_sphericity_bonded	16.485
r_dihedral_angle_3_deg	11.197
r_dihedral_angle_1_deg	7.645
r_mcangle_it	3.656
r_mcbond_it	2.943
r_mcbond_other	2.941
r_rigid_bond_restr	2.817
r_angle_other_deg	1.86
r_angle_refined_deg	1.779
r_chiral_restr	0.169
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1248
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms

Software

Software
Software Name	Purpose
SERGUI	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

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.