1VL6 | pdb_00001vl6

Crystal structure of NAD-dependent malic enzyme (TM0542) from Thermotoga maritima at 2.61 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	0.025M Citric Acid, 0.075M Citrate_Na3, 6.00% NP_Peg 6000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	0.025M Citric Acid, 0.075M Citrate_Na3, 6.00% NP_Peg 6000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.87
3.12	60.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.963	α = 90
b = 143.963	β = 90
c = 163.428	γ = 120

Symmetry
Space Group	P 65

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		2003-07-25	M	SINGLE WAVELENGTH
2	1	x-ray	100	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.019943, 0.979762, 0.979619	ALS	8.3.1

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	2.6	47.12	98.84	0.054	16.77	3.26		57871			74.19

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)
1,2	2.6	2.69	96.26		0.551	1.84	2.86	5591

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	MAD	THROUGHOUT	2.61	47.12	55267	2333	98.53	0.1938	0.19189	0.2	0.23929	0.23	RANDOM	61.902

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]
1.1	0.55		1.1		-1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.556
r_dihedral_angle_3_deg	17.945
r_dihedral_angle_4_deg	17.668
r_scangle_it	8.133
r_dihedral_angle_1_deg	6.65
r_scbond_it	5.8
r_mcangle_it	2.64
r_angle_refined_deg	1.658
r_mcbond_it	1.521
r_angle_other_deg	0.933
r_mcbond_other	0.492
r_symmetry_vdw_refined	0.4
r_symmetry_vdw_other	0.274
r_nbd_refined	0.236
r_nbtor_refined	0.189
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.096
r_symmetry_hbond_refined	0.094
r_nbtor_other	0.091
r_xyhbond_nbd_other	0.065
r_bond_refined_d	0.017
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	11096
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
MOSFLM	data reduction
SCALEPACK	data scaling
SOLVE	phasing
SHARP	phasing
REFMAC	refinement