9HRE | pdb_00009hre

Peptide-substrate-binding (PSB) domain of human type I collagen prolyl 4-hydroxylase complexed with Pro-Hyp-Gly-Pro-Ala-Gly-Pro-Hyp-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	7	278	30% MPD, 48 mM MgCl2, 50 mM KCl, 100 mM MOPS, 5 mM peptide (POG-PAG-POG)

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.041	α = 90
b = 85.561	β = 90
c = 92.506	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 EIGER X 16M	Toroidal mirror	2018-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

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	2.05	92.51	98.8	0.072	0.03	0.999	14.8	6.6		40436			46.01

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	2.05	2.11	97.2		1.65	0.676	0.468	1.6	6.8

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	2.05	62.89	40403	1965	98.52	0.198	0.1972	0.1972	0.218	0.2181	Random selection	60.834

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]
1.25			1.176		-2.426

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.276
r_dihedral_angle_3_deg	14.504
r_lrange_it	12.125
r_lrange_other	12.11
r_dihedral_angle_2_deg	10.872
r_scangle_it	9.996
r_scangle_other	9.994
r_scbond_it	6.489
r_scbond_other	6.488
r_mcangle_other	5.674
r_mcangle_it	5.672
r_dihedral_angle_1_deg	4.99
r_mcbond_other	4.204
r_mcbond_it	4.203
r_angle_refined_deg	1.686
r_angle_other_deg	0.565
r_nbd_refined	0.231
r_nbtor_refined	0.191
r_symmetry_nbd_other	0.18
r_xyhbond_nbd_refined	0.173
r_nbd_other	0.151
r_symmetry_xyhbond_nbd_refined	0.147
r_symmetry_nbd_refined	0.14
r_ncsr_local_group_4	0.122
r_ncsr_local_group_6	0.121
r_ncsr_local_group_1	0.108
r_ncsr_local_group_3	0.108
r_ncsr_local_group_2	0.091
r_ncsr_local_group_5	0.085
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.074
r_metal_ion_refined	0.059
r_symmetry_xyhbond_nbd_other	0.055
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3466
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	149

Software

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