7H6D | pdb_00007h6d

THE 1.64 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH 1-[(8-methylnaphthalen-1-yl)methyl]indole-2-carboxylic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.5	293	Sample of human Chymase in 50 mM MES/NaOH pH 5.5, 150mM NaCl, 1mM TCEP, 10% Glycerol) at a concentration of 11mg/ml to 14mg/ml.Add [2-[(4-methylpyridin-2-yl)amino]-2-oxoethyl] 2-methylquinoline-4-carboxylate at 10x molar ratio. The compound helps to obtain crystals but is not visible in the structures. Add 0.5 mM ZnCl2. Add inhibitor, incubate for 16h on ice. Crystallize using microbatch setups with Al's oil (Hampton Research), with total drop size 1ul with 50% protein sample, using crystallization reagent of 0.1M Tris/HCl pH 8.5, 0.2M NaCl, 25% PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.53	α = 90
b = 74.53	β = 90
c = 49.53	γ = 90

Symmetry
Space Group	P 43

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	MAR scanner 345 mm plate		2006-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.64	18.64	98.3	0.047	0.051	29.82			32893

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.74		92.5	0.255	0.277

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.64	18.64	31228	1662	98.97	0.14867	0.14735	0.161	0.17343	0.1853	RANDOM	11.962

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			-0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	9.982
r_dihedral_angle_1_deg	6.908
r_dihedral_angle_2_deg	6.04
r_long_range_B_refined	4.349
r_long_range_B_other	3.886
r_scangle_other	2.211
r_angle_refined_deg	1.579
r_mcangle_other	1.495
r_mcangle_it	1.494
r_scbond_it	1.375
r_scbond_other	1.374
r_mcbond_it	0.934
r_mcbond_other	0.934
r_angle_other_deg	0.756
r_chiral_restr	0.078
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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	1759
Nucleic Acid Atoms
Solvent Atoms	337
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing