9HT8 | pdb_00009ht8

Peptide-substrate-binding (PSB) domain of human type I collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Ala-Gly-Pro-Pro-Gly.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V5F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	278	30% MPD, 50 mM MgCl2, 50 mM KCl, 100 mM MOPS

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.64	α = 90
b = 84.64	β = 90
c = 90.166	γ = 90

Symmetry
Space Group	P 42 21 2

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 2M	Vertical CRL, horizontal CRL	2022-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9655	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	90.17	99.5	0.053	0.017	0.999	19.8	10.9		18422			63.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	96.6		2.275	0.713	0.548	1	10.9

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	2.15	59.921	18369	920	99.712	0.2	0.1977	0.1978	0.2408	0.2411	83.052

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]
0.815			0.815		-1.629

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.161
r_dihedral_angle_6_deg	17.152
r_dihedral_angle_3_deg	16.249
r_lrange_other	11.947
r_lrange_it	11.945
r_scangle_it	9.327
r_scangle_other	9.324
r_mcangle_it	6.787
r_mcangle_other	6.784
r_scbond_it	6.338
r_scbond_other	6.335
r_dihedral_angle_1_deg	6.235
r_mcbond_it	4.83
r_mcbond_other	4.796
r_angle_refined_deg	1.625
r_angle_other_deg	0.621
r_nbd_refined	0.21
r_nbtor_refined	0.178
r_nbd_other	0.17
r_symmetry_xyhbond_nbd_refined	0.168
r_symmetry_nbd_other	0.161
r_xyhbond_nbd_refined	0.129
r_symmetry_nbd_refined	0.129
r_ncsr_local_group_1	0.117
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.07
r_metal_ion_refined	0.02
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1742
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	85

Software

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