4LP9 | pdb_00004lp9

Endothiapepsin complexed with Phe-reduced-Tyr peptide.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GVX	PDB ENTRY 1GVX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.9	294	0.1 M sodium acetate, 63% saturated ammonium sulfate, 3 mg/ml enzyme, 2 mM inhibitor (dissolved initially in DMSO), pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.62	α = 90
b = 72.787	β = 108.54
c = 45.113	γ = 90

Symmetry
Space Group	P 1 21 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	PSI PILATUS 6M			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	1.0435	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.35	28.32	98.2	0.047	0.047	14.8	3.3	69622	69622			11.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.38	84.1		0.571	0.571	2.1	2.3	4381

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1GVX	1.35	27.72	70843	66078	3576	98.42	0.1252	0.1231	0.12	0.1649	0.17	RANDOM	16.182

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]
0.06		-0.03	-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.192
r_dihedral_angle_2_deg	30.028
r_dihedral_angle_4_deg	23.079
r_sphericity_bonded	12.406
r_dihedral_angle_3_deg	11.02
r_dihedral_angle_1_deg	6.5
r_rigid_bond_restr	5.698
r_long_range_B_refined	5.363
r_long_range_B_other	5.351
r_scangle_other	4.011
r_scbond_it	3.814
r_scbond_other	3.808
r_mcangle_other	2.472
r_mcangle_it	2.466
r_angle_refined_deg	2.112
r_mcbond_it	2.059
r_mcbond_other	1.952
r_angle_other_deg	1.018
r_chiral_restr	0.129
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_bond_other_d	0.004
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2461
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	51

Software

Software
Software Name	Purpose
GDA	data collection
FFT	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
FFT	phasing