2VVR | pdb_00002vvr

Crystal structure of the H99N mutant of ribose-5-phosphate isomerase B from E. coli soaked with ribose 5-phosphate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NN4	PDB ENTRY 1NN4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				20% PEG 3350, 0.1 M MES PH6

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.701	α = 90
b = 51.862	β = 115.55
c = 207.209	γ = 90

Symmetry
Space Group	C 1 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	110	CCD	ADSC CCD		2007-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	2.1	40.49	99.9	0.11	14.1	3.6		50635		5.8	19.1

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	2.1	2.21	99.9		0.17	5.8	3.6

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	PDB ENTRY 1NN4	2.1	40	48057	2574	99.9	0.19	0.188	0.19	0.237	0.24	RANDOM	13.77

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]
-0.43		-0.19	-0.61		0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.444
r_dihedral_angle_4_deg	19.164
r_dihedral_angle_3_deg	12.654
r_dihedral_angle_1_deg	5.589
r_scangle_it	2.571
r_scbond_it	1.786
r_angle_refined_deg	1.175
r_mcangle_it	0.999
r_angle_other_deg	0.95
r_mcbond_it	0.87
r_symmetry_vdw_other	0.212
r_nbd_refined	0.196
r_nbd_other	0.184
r_nbtor_refined	0.171
r_symmetry_vdw_refined	0.166
r_symmetry_hbond_refined	0.153
r_mcbond_other	0.128
r_xyhbond_nbd_refined	0.126
r_nbtor_other	0.083
r_chiral_restr	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6621
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing