7JRH | pdb_00007jrh

X-ray crystal structure of a cyclic peptide containing medin(19-25) and medin(31-37)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.1 M NaOAc, 0.02M CaCl2, 30% MPD

Crystal Properties
Matthews coefficient	Solvent content
1.73	28.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.486	α = 90
b = 42.486	β = 90
c = 42.486	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	APEX II CCD		2020-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.32	30.09	99.74	0.04568	0.04648	0.008085	1	30.81	16.6		51865			15.04

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.321	1.368	97.83		0.3153	0.3423	0.1275	0.925	3.32	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO PHASING	FREE R-VALUE	1.32	30.04	1.44	3117	315	99.74	0.1808	0.1772	0.18	0.2103	0.21	18.59

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	35.9682
f_angle_d	1.5117
f_chiral_restr	0.0913
f_bond_d	0.0092
f_plane_restr	0.0058

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	130
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
SAINT	data reduction
SADABS	data scaling
AutoSol	phasing