4XG1 | pdb_00004xg1

Psychromonas ingrahamii diaminopimelate decarboxylase with LLP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N2B	PDB ID 3N2B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	281	28%(W/V) PEG 3350, 100mM BIS-TRIS PROPANE (PH 6.0), 200mM POTASSIUM THIOCYANATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.96	α = 90
b = 103.13	β = 94.77
c = 93.59	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r		2014-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.954	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	69.17	99.8	0.072	0.077	20.3	7.3		58922

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	99.9		0.146	0.157	11.6	7.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 3N2B	2.5	19.85	57729	1014	99.49	0.2119	0.2113	0.21	0.24589	0.25	RANDOM	31.382

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]
0.07		0.09	-0.03		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.689
r_dihedral_angle_4_deg	18.905
r_dihedral_angle_3_deg	15.737
r_long_range_B_refined	6.887
r_long_range_B_other	6.886
r_dihedral_angle_1_deg	6.591
r_scangle_other	4.399
r_mcangle_it	4.294
r_mcangle_other	4.294
r_mcbond_it	2.688
r_mcbond_other	2.688
r_scbond_it	2.636
r_scbond_other	2.635
r_angle_refined_deg	1.506
r_angle_other_deg	1.116
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.006
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	12467
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	148

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
Coot	model building
XDS	data reduction
Auto-Rickshaw	phasing