8B30 | pdb_00008b30

Structure of the Reconstructed Ancestor of Phenolic Acid Decarboxylase AncPAD31

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	5 mg/ml AncPAD31, Index screen 74, 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS, 25% w/v Polyethylene glycol 3,350

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.069	α = 90
b = 59.971	β = 90
c = 105.1	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	100	PIXEL	Bruker PHOTON III		2021-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34138

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	2.7	34.98	99.9	0.135	0.157	0.078	0.995	5.6	6.7		7936

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	2.7	2.83			0.867	1.011	0.508	0.703		6.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4UU3	2.7	34.98	7901	384	99.899	0.214	0.2102	0.21	0.2841	0.28	47.72

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]
-0.656			1.492		-0.835

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.918
r_dihedral_angle_4_deg	27.369
r_dihedral_angle_3_deg	19.109
r_lrange_it	13.719
r_lrange_other	13.705
r_scangle_other	10.634
r_scangle_it	10.633
r_dihedral_angle_1_deg	8.922
r_mcangle_it	8.382
r_mcangle_other	8.38
r_scbond_it	7.26
r_scbond_other	7.253
r_mcbond_it	6.018
r_mcbond_other	6.007
r_angle_other_deg	2.457
r_angle_refined_deg	2.124
r_nbd_other	0.288
r_symmetry_nbd_other	0.217
r_symmetry_xyhbond_nbd_refined	0.204
r_nbd_refined	0.197
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.161
r_ncsr_local_group_1	0.157
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.062
r_bond_other_d	0.035
r_gen_planes_other	0.017
r_bond_refined_d	0.014
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2603
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
PROTEUM	data reduction
PROTEUM	data scaling
PHASER	phasing