8JIJ | pdb_00008jij

Alanine decarboxylase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		8JG7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	3.5M Sodium formate, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
4.13	70.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.485	α = 90
b = 163.485	β = 90
c = 50.203	γ = 120

Symmetry
Space Group	P 31 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 PILATUS3 6M		2021-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.979	SSRF	BL18U1

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	2.5	50	99.3	0.128	0.141	0.06	0.973	3.2	5.4		26556

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	2.5	2.54	99.9		0.603	0.672	0.292	0.754		5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.5	17.57	25175	1369	99.25	0.17517	0.17278	0.1789	0.22213	0.2229	RANDOM	40.443

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]
0.61	0.31		0.61		-1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.935
r_dihedral_angle_2_deg	11.292
r_long_range_B_refined	7.868
r_long_range_B_other	7.868
r_dihedral_angle_1_deg	7.188
r_scangle_other	6.118
r_mcangle_it	5.203
r_mcangle_other	5.202
r_scbond_other	4.12
r_scbond_it	4.118
r_mcbond_it	3.427
r_mcbond_other	3.409
r_angle_refined_deg	1.531
r_angle_other_deg	0.621
r_chiral_restr	0.075
r_bond_other_d	0.011
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3288
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing