3IXQ

Structure of ribose 5-phosphate isomerase a from methanocaldococcus jannaschii

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	oil batch (TERA)	4.75	298	20MM TRIS-HCL PH 8.0, 200MM NACL. 40% V/V 1,2-PROPANEDIOL, 0.1M ACETATE PH 4.5, 0.05M CA ACETATE, oil batch (TERA), temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.856	α = 90
b = 100.273	β = 92.54
c = 80.465	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD	mirrors	2007-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.074	SRS	PX10.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	30	98.5	0.104	0.087	13.6	8	94575	94575			17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.76	98.3		0.392	0.38	4	5.1	8356

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1KL5	1.78	30	81022	81022	4045	97.57	0.15	0.15	0.148	0.188	RANDOM	17.944

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]
0.42		0.66	-0.6		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.39
r_dihedral_angle_4_deg	15.181
r_dihedral_angle_3_deg	12.942
r_dihedral_angle_1_deg	6.038
r_scangle_it	3.246
r_scbond_it	2.346
r_angle_refined_deg	1.469
r_mcangle_it	1.31
r_mcbond_it	1.186
r_angle_other_deg	1.015
r_symmetry_vdw_refined	0.286
r_symmetry_vdw_other	0.267
r_mcbond_other	0.225
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.199
r_nbd_other	0.191
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.088
r_nbtor_other	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7259
Nucleic Acid Atoms
Solvent Atoms	889
Heterogen Atoms	69

Software

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