6KBR

Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Lithium chloride, polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.208	α = 90
b = 41.62	β = 91.58
c = 43.59	γ = 90

Symmetry
Space Group	C 1 2 1

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 2M-F		2017-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1	Photon Factory	AR-NE3A

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	1.9	72.577	99.6	0.099	8.8	3.4		20687

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	1.9	1.94			0.245

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2BDG	2	72.577	16901	897	99.72	0.18747	0.18541	0.22584	RANDOM	10.645

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]
		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.477
r_dihedral_angle_4_deg	19.053
r_dihedral_angle_3_deg	15.181
r_dihedral_angle_1_deg	7.107
r_long_range_B_refined	3.908
r_long_range_B_other	3.907
r_scangle_other	2.704
r_angle_refined_deg	1.977
r_mcangle_it	1.731
r_mcangle_other	1.73
r_scbond_it	1.705
r_scbond_other	1.705
r_angle_other_deg	1.092
r_mcbond_it	1.055
r_mcbond_other	1.054
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2078
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
MOLREP	phasing