9IBU | pdb_00009ibu

THE COLLAGEN REPEATING SEQUENCE (PRO-PRO-GLY)10 AT HIGH RESOLUTION

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K6F	N-term and C-term PPG triplets removed

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	In 9 well Glass Plates (wells are vapor-connected 3 by 3). Well-A..Well-B..Well-C. In well-A: 150 muL monoglyme, in well-B: 150 muL water, in well-C: 20 muL PPG solution (6 mg/mL in acetic acid 10%).

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.923	α = 90
b = 26.377	β = 90
c = 182.873	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 EIGER X 9M		2018-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.9537	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.1	55.5	82.9	0.062	0.052	0.058	0.998	10.3	8.1		57261			12.2

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	1.1	1.17	63.9		0.38	0.963	1.9	6.2

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	FREE R-VALUE	1.25	45.718	32190	1598	86.076	0.204	0.2029	0.1976	0.2321	0.1878	13.653

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]
0.005			-0.168		0.163

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	13.527
r_lrange_other	13.413
r_rigid_bond_restr	6.364
r_scangle_it	6.062
r_scangle_other	6.059
r_mcangle_it	5.563
r_mcangle_other	5.562
r_dihedral_angle_1_deg	5.206
r_scbond_it	4.24
r_scbond_other	4.221
r_mcbond_it	3.862
r_mcbond_other	3.846
r_angle_refined_deg	1.733
r_angle_other_deg	0.962
r_symmetry_nbd_refined	0.401
r_symmetry_xyhbond_nbd_other	0.339
r_nbd_other	0.268
r_xyhbond_nbd_refined	0.25
r_symmetry_xyhbond_nbd_refined	0.241
r_xyhbond_nbd_other	0.201
r_nbd_refined	0.198
r_nbtor_refined	0.187
r_symmetry_nbd_other	0.18
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
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	353
Heterogen Atoms

Software

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