Experiment: 8DSL

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	Hampton Research Cryschem 24-well plates. 1.5 uL of WT PHM protein at 17 mg/mL in 20 mM sodium phosphate, pH 7.5 was added to 1.5 uL of mother liquor solution containing 16-18% PEG 20K, 20-250 mM sodium citrate, and 2 mM CuSO4. Plates were sealed using transparent tape. Crystals were formed within one week, and these initial crystals were used to seed succeeding trays using the same crystal conditions. Seeding was performed using a Hampton Research seed bead and Hampton Research seeding tool. Initial crystals (5-7 crystals) were vortexed with seed beads for 30 seconds in 30 uL mother liquor, and streaked into a new drop using the seeding tool.

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.166	α = 85.03
b = 53.535	β = 89.79
c = 86.139	γ = 77.62

Symmetry
Space Group	P 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 PILATUS3 6M		2021-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.05	38.25	98.1	0.071	0.076	0.025	0.999	15.9	8.9		41882

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11	96.8		0.539	0.574	0.194	0.95	3.5	8.7

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	1phm	2.05	38.25	39833	2063	98.07	0.198	0.1959	0.2392	RANDOM	43.646

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]
-0.05	0.03		-0.02	-0.07	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.833
r_dihedral_angle_3_deg	18.064
r_dihedral_angle_4_deg	14.06
r_dihedral_angle_1_deg	8.252
r_angle_refined_deg	1.701
r_angle_other_deg	1.271
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.833
r_dihedral_angle_3_deg	18.064
r_dihedral_angle_4_deg	14.06
r_dihedral_angle_1_deg	8.252
r_angle_refined_deg	1.701
r_angle_other_deg	1.271
r_chiral_restr	0.079
r_bond_refined_d	0.01
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	4836
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	16

Software

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