5RDX

PanDDA analysis group deposition -- Endothiapepsin ground state model 54

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	290	0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.222	α = 90
b = 72.931	β = 109.07
c = 52.336	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	DECTRIS EIGER X 16M		2019-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.827	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	0.98	49.51	93.3	0.064	0.07	0.999	11.47	6.786		164172			15.302

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.98	1.04	0.726		2.886	3.183	0.179	0.56	4.11	29894

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	0.98	49.51	164172	8666	93.4	0.1604	0.15963	0.16041	RANDOM	12.597

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]
-0.32		-0.3	0.01		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.928
r_dihedral_angle_4_deg	17.089
r_dihedral_angle_3_deg	9.035
r_dihedral_angle_1_deg	6.802
r_angle_refined_deg	1.911
r_angle_other_deg	1.647
r_mcangle_it	1.621
r_mcbond_it	1.125
r_mcbond_other	1.122
r_chiral_restr	0.101
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2369
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing
PHENIX	refinement