9I9A | pdb_00009i9a

COLLAGEN-LIKE (PRO-PRO-GLY)10 AT 0.86 GPa HYDROSTATIC PRESSURE

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K6F	CRYSTAL STRUCTURE OF THE COLLAGEN TRIPLE HELIX MODEL [(PRO-PRO-GLY)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	IN a three-well (connected as well#1-well#2-well#3) glass plate: 20 mu-L PPG solution (10mg/mL in acetic acid 10%) in well#1. 150 mu-L Water in well#2 and 150 mu-L monoglyme in well#3. Monoglyme diffuses in well#2 then well#1. Crystals as small cubes in a week.

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.2	α = 90
b = 25.75	β = 90
c = 180.49	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	291	PIXEL	DECTRIS EIGER2 X CdTe 9M		2023-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID27	0.410	ESRF	ID27

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.7	24.8	79.7	0.093	0.995	4.2	3.8		27472			13.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.744	86.4		0.35	0.995	2.4	3.5

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	1.7	24.762	12140	608	84.711	0.203	0.1999	0.2012	0.2555	0.2524	12.254

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]
0.12			-0.408		0.289

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.29
r_lrange_other	15.176
r_dihedral_angle_1_deg	7.27
r_mcangle_other	5.157
r_mcangle_it	5.155
r_scangle_it	3.574
r_scangle_other	3.572
r_mcbond_it	3.264
r_mcbond_other	3.238
r_rigid_bond_restr	2.513
r_scbond_it	2.2
r_scbond_other	2.168
r_angle_refined_deg	1.51
r_angle_other_deg	0.913
r_symmetry_nbd_refined	0.33
r_xyhbond_nbd_other	0.294
r_symmetry_xyhbond_nbd_refined	0.225
r_nbd_refined	0.22
r_nbd_other	0.22
r_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.188
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.098
r_gen_planes_refined	0.01
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1140
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing