9HPQ | pdb_00009hpq

Peptide-substrate-binding (PSB) domain of human type I collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Arg-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	1TJC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	278	30% MPD, 50 mM MgCl2, 50 mM KCl, 100 mM MOPS

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.418	α = 90
b = 86.315	β = 90
c = 91.132	γ = 90

Symmetry
Space Group	P 21 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	CRL	2017-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

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	2.17	49.88	99.6	0.058	0.999	13.5	4.7		34940			52.8

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	2.17	2.25	99.6		1.412	0.482	1.1	4.7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.17	49.88	34846	1726	99.387	0.226	0.225	0.2277	0.2499	0.2521	Random selection	63.77

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]
-0.606			-1.1		1.706

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.629
r_dihedral_angle_3_deg	15.195
r_dihedral_angle_2_deg	13.461
r_lrange_it	9.373
r_lrange_other	9.372
r_scangle_it	6.239
r_scangle_other	6.238
r_dihedral_angle_1_deg	4.942
r_scbond_it	4.046
r_scbond_other	4.033
r_mcangle_it	3.656
r_mcangle_other	3.655
r_mcbond_it	2.432
r_mcbond_other	2.432
r_angle_refined_deg	1.525
r_angle_other_deg	0.522
r_nbd_refined	0.222
r_nbtor_refined	0.185
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.178
r_symmetry_nbd_other	0.175
r_symmetry_nbd_refined	0.138
r_ncsr_local_group_6	0.112
r_ncsr_local_group_4	0.104
r_ncsr_local_group_2	0.098
r_ncsr_local_group_3	0.093
r_ncsr_local_group_1	0.092
r_ncsr_local_group_5	0.09
r_metal_ion_refined	0.078
r_chiral_restr	0.073
r_symmetry_nbtor_other	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3453
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	149

Software

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