1VMD | pdb_00001vmd

Crystal structure of Methylglyoxal synthase (TM1185) from Thermotoga maritima at 2.06 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B93

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	5.5	277	15.0% Ethanol, 0.2M Li2SO4, 0.1M Citrate pH 5.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.43	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.243	α = 90
b = 130.243	β = 90
c = 130.243	γ = 90

Symmetry
Space Group	I 2 3

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		2004-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	91.89	98.4	0.111	9.2	5		22616			44.63

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.1	87.4		0.701	0.8	2	1449

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	1b93	2.06	91.89	21411	1163	98.03	0.16998	0.16732	0.18	0.21884	0.23	RANDOM	40.559

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.898
r_dihedral_angle_4_deg	16.375
r_dihedral_angle_3_deg	16.318
r_scangle_it	7.411
r_dihedral_angle_1_deg	6.145
r_scbond_it	5.323
r_mcangle_it	2.922
r_mcbond_it	2.293
r_angle_refined_deg	1.57
r_angle_other_deg	0.885
r_mcbond_other	0.673
r_symmetry_vdw_other	0.229
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.191
r_nbd_other	0.178
r_nbtor_refined	0.173
r_symmetry_hbond_refined	0.165
r_symmetry_vdw_refined	0.115
r_chiral_restr	0.096
r_nbtor_other	0.083
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2488
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling