5GJP | pdb_00005gjp

Crystal structure of SrLDC in complex with PLP and Cadaverine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GJN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	293	PEG 200, Sodium phosphate, NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.734	α = 90
b = 111.734	β = 90
c = 112.976	γ = 120

Symmetry
Space Group	P 63 2 2

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 270		2015-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	50	96.8	0.132	27.8	24.2		14439

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	95.1		0.317	0.907		12.9

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	5GJN	2.5	50	13670	766	96.76	0.2003	0.1979	0.1983	0.2786	0.2786	RANDOM	52.041

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]
1.45	0.72		1.45		-4.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.543
r_dihedral_angle_4_deg	18.14
r_dihedral_angle_3_deg	17.295
r_dihedral_angle_1_deg	6.892
r_mcangle_it	5.361
r_mcbond_it	3.547
r_mcbond_other	3.546
r_angle_refined_deg	1.636
r_angle_other_deg	1.015
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2948
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction