5QR4 | pdb_00005qr4

PanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z2856434826

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	0.1 M HEPES pH 7.5, 0.2 M magnesium chloride, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.359	α = 90
b = 108.967	β = 109.32
c = 76.099	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS 6M		2019-04-05		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.572	60.094	95.1	0.048	0.025	0.999	14.3	3.4		97789

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.572	1.696	72.2		0.778	0.433	0.662		3.1	4889

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	FOURIER SYNTHESIS	THROUGHOUT	6hrh	1.57	60.17	92970	4834	71.7	0.2149	0.2138	0.23	0.2381	0.25	RANDOM	26.526

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]
0.21		0.05	-0.14		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.629
r_dihedral_angle_4_deg	20.155
r_dihedral_angle_3_deg	15.387
r_dihedral_angle_1_deg	6.773
r_mcangle_it	3.08
r_mcbond_it	2.191
r_mcbond_other	2.191
r_angle_refined_deg	1.614
r_angle_other_deg	1.41
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.629
r_dihedral_angle_4_deg	20.155
r_dihedral_angle_3_deg	15.387
r_dihedral_angle_1_deg	6.773
r_mcangle_it	3.08
r_mcbond_it	2.191
r_mcbond_other	2.191
r_angle_refined_deg	1.614
r_angle_other_deg	1.41
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6605
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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 R01GM157729.