9GCD | pdb_00009gcd

CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH Fulacimstat (COMPOUND86)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in-house Model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	0.01M ZnCl2, 0.1M TRIS at pH 8 and 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.08	α = 90
b = 74.08	β = 90
c = 49.79	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		2011-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.541870

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	1.79	41.32	98.2	0.051	14.3	2.6		24967

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	1.79	1.89			0.318	3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.798	29.718	24925	1273	98.639	0.179	0.1778	0.1779	0.212	0.2121	33.036

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]
0.031			0.031		-0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.629
r_dihedral_angle_4_deg	19.783
r_dihedral_angle_3_deg	12.384
r_lrange_it	7.134
r_dihedral_angle_1_deg	6.792
r_scangle_it	5.774
r_scbond_it	3.836
r_mcangle_it	2.741
r_mcbond_it	2.141
r_angle_refined_deg	1.603
r_nbtor_refined	0.314
r_nbd_refined	0.271
r_symmetry_xyhbond_nbd_refined	0.271
r_symmetry_nbd_refined	0.242
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.083
r_metal_ion_refined	0.049
r_symmetry_metal_ion_refined	0.047
r_bond_refined_d	0.013
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1666
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	114

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing