2I2C | pdb_00002i2c

Crystal structure of LmNADK1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I2B	PDB ENTRY 2I2B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4		0.3 M POTASSIUM CHLORIDE, 50 MM TRI-SODIUM CITRATE DIHYDRATE, 15-20% W/V POLYETHYLENE GLYCOL 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.07	α = 90
b = 75.297	β = 90
c = 118.65	γ = 90

Symmetry
Space Group	I 2 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 315		2006-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.9793	ESRF	ID14-2

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	1.85	25.3	98.9	0.068	17.3	5.2		22941			27.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.95	93.5		0.442	1.9	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 ENTRY 2I2B	1.85	23.29	24181	22941	1240	98.69	0.192	0.192	0.191	0.1907	0.21	0.2094	RANDOM	32.272

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]
0.55			1.88		-2.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.946
r_dihedral_angle_4_deg	15.501
r_dihedral_angle_3_deg	14.977
r_dihedral_angle_1_deg	10.268
r_angle_refined_deg	1.451
r_scangle_it	1.195
r_scbond_it	0.883
r_mcangle_it	0.683
r_mcbond_it	0.424
r_nbtor_refined	0.313
r_xyhbond_nbd_refined	0.255
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.175
r_chiral_restr	0.152
r_symmetry_hbond_refined	0.107
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2073
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing