7DZZ | pdb_00007dzz

Trans-3/4-proline-hydroxylase H11-stateV

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7DT0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289.15	0.7 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.664	α = 90
b = 106.664	β = 90
c = 143.893	γ = 90

Symmetry
Space Group	P 41 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		2020-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.979	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	85.69	92.5	0.099	16.9	13.1		56700

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.05			1.207	0.346

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7DT0	1.95	85.69	54027	2743	92.51	0.2049	0.203	0.2136	0.2417	0.2508	RANDOM	44.203

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]
0.85			0.85		-1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.587
r_dihedral_angle_4_deg	17.587
r_dihedral_angle_3_deg	16.921
r_dihedral_angle_1_deg	7.777
r_angle_refined_deg	2.051
r_angle_other_deg	1.129
r_chiral_restr	0.132
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4147
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing