7N7X | pdb_00007n7x

Crystal structure of BCX7353(ORLADEYO) in complex with human plasma kallikrein serine protease domain at 2.1 angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	290	25% PEG 6000, 0.1MES buffer

Crystal Properties
Matthews coefficient	Solvent content
2.48	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.726	α = 90
b = 59.752	β = 90
c = 79.023	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	PIXEL	DECTRIS PILATUS 200K	osmic mirrors	2017-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5180

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.09	40.39	97.6	0.069	0.031	0.963	37.7	3.9		15531	3		23.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.16	85		0.169	0.108	0.963	9	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2ANY	2.097	40.39	3	15472	769	98.21	0.202	0.1991	0.21	0.2592	0.27	25.053

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]
-0.001					0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.885
r_dihedral_angle_3_deg	14.913
r_dihedral_angle_4_deg	13.985
r_dihedral_angle_1_deg	8.424
r_lrange_it	6.732
r_lrange_other	6.716
r_scangle_it	4.504
r_scangle_other	4.496
r_mcangle_other	4.06
r_mcangle_it	4.056
r_scbond_it	2.772
r_scbond_other	2.763
r_mcbond_it	2.486
r_mcbond_other	2.46
r_chiral_restr_other	1.647
r_angle_refined_deg	1.623
r_angle_other_deg	1.362
r_nbd_refined	0.209
r_nbd_other	0.196
r_symmetry_nbd_other	0.186
r_symmetry_nbd_refined	0.182
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1828
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing