7QZJ

1.55 A X-ray crystallographic structure of SapH from Streptomyces sp. (HPH0547) involved in Pseudouridimycin biosynthesis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.1M BTP pH 7.5 0.2M Na-K-Phosphate 27.5% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.581	α = 90
b = 63.191	β = 90
c = 211.415	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	110	PIXEL	DECTRIS EIGER X 16M	KB mirrors	2020-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.97625	MAX IV	BioMAX

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	1.55	44.47	98.8	0.079	0.046	0.997	11.1	6.4		121033	1.5	1.5	15.8

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	1.55	1.58	88.7		0.598	0.509	0.679	1.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5GHG	1.55	44.47	114927	5991	98.71	0.1606	0.1595	0.1823	RANDOM	23.519

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]
0.15			0.85		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.915
r_dihedral_angle_4_deg	14.069
r_dihedral_angle_3_deg	12.082
r_dihedral_angle_1_deg	5.717
r_angle_refined_deg	1.421
r_angle_other_deg	0.957
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.915
r_dihedral_angle_4_deg	14.069
r_dihedral_angle_3_deg	12.082
r_dihedral_angle_1_deg	5.717
r_angle_refined_deg	1.421
r_angle_other_deg	0.957
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6275
Nucleic Acid Atoms
Solvent Atoms	894
Heterogen Atoms	47

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.