9GHY | pdb_00009ghy

Cyclophilin A in complex with Sanglifehrin A analogue (2R,3S,7S,10S,E)-10-(3-aminopropyl)-2,7-dimethylspiro[3,8,11-triaza-1(2,7)-quinolina-5(3,1)-pyridazinacyclopentadecaphanene-13,5'-[1,3]dioxan]-14-ene-4,6,9,12-tetraone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6X4N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	28% PEG-3350, 0.1 M Tris-HCl pH 8.8

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.854	α = 90
b = 52.595	β = 90
c = 89.257	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 S 6M		2022-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918400	BESSY	14.1

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	1.15	45.31	98.8	0.038	0.044	0.022	1	18.9	7.2		71497

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	1.15	1.17			1.342	1.562	0.789	0.712		7.2

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	THROUGHOUT	1.15	45.004	71430	3671	98.653	0.132	0.1309	0.1399	0.149	0.1519	19.689

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]
-0.899			1.746		-0.847

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.014
r_dihedral_angle_6_deg	13.863
r_lrange_other	12.811
r_dihedral_angle_3_deg	9.7
r_scangle_it	8.466
r_scangle_other	8.462
r_dihedral_angle_2_deg	7.653
r_dihedral_angle_1_deg	6.26
r_scbond_it	6.142
r_scbond_other	6.139
r_mcangle_it	6.133
r_mcangle_other	6.129
r_mcbond_it	4.66
r_mcbond_other	4.657
r_rigid_bond_restr	3.903
r_angle_refined_deg	1.86
r_chiral_restr_other	1.107
r_angle_other_deg	0.813
r_nbd_refined	0.261
r_symmetry_xyhbond_nbd_refined	0.218
r_symmetry_nbd_other	0.21
r_symmetry_xyhbond_nbd_other	0.188
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.156
r_nbd_other	0.149
r_chiral_restr	0.108
r_symmetry_nbtor_other	0.089
r_symmetry_nbd_refined	0.027
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1267
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
autoXDS	data reduction
Aimless	data scaling
PHASER	phasing