3M4R | pdb_00003m4r

Structure of the N-terminal Class II Aldolase domain of a conserved protein from Thermoplasma acidophilum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.1M Bis-Tris Propane pH 7.0, 3.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.136	α = 90
b = 46.136	β = 90
c = 203.998	γ = 120

Symmetry
Space Group	P 32 2 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 210r		2009-06-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97970, 0.97945	APS	19-BM

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	50	99.7	0.074	12.3	10.6	18049	18049		-3	36.4

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	2.03	99.8		0.622	3.8	10.9	856

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2	25.89	17900	17900	913	99.82	0.188	0.188	0.186	0.2217	0.233	0.2614	RANDOM	27.496

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]
1.63	0.81		1.63		-2.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.871
r_dihedral_angle_4_deg	17.882
r_dihedral_angle_3_deg	15.527
r_dihedral_angle_1_deg	5.52
r_scangle_it	3.393
r_scbond_it	2.263
r_angle_refined_deg	1.497
r_mcangle_it	1.403
r_angle_other_deg	0.922
r_mcbond_it	0.826

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.871
r_dihedral_angle_4_deg	17.882
r_dihedral_angle_3_deg	15.527
r_dihedral_angle_1_deg	5.52
r_scangle_it	3.393
r_scbond_it	2.263
r_angle_refined_deg	1.497
r_mcangle_it	1.403
r_angle_other_deg	0.922
r_mcbond_it	0.826
r_mcbond_other	0.228
r_chiral_restr	0.09
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1612
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.