2RB9 | pdb_00002rb9

Crystal structure of E.coli HypE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I6R	PDB entry 2I6R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	0.6M Na/K phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 254.574	α = 90
b = 72.303	β = 115.33
c = 112.607	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	100	CCD	MAR CCD 165 mm		2007-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	1.00000	APS	31-ID

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	1.6	50	81.7	0.068	7.5	3.4		196364

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)
	1.6	1.66	9.4		0.596		1.2	2246

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 2I6R	2	43.73	123532	6153	98.72	0.177	0.176	0.1787	0.208	0.21	RANDOM	25.337

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]
-0.02			0.03		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.017
r_dihedral_angle_4_deg	15.519
r_dihedral_angle_3_deg	13.415
r_dihedral_angle_1_deg	5.321
r_scangle_it	3.52
r_scbond_it	2.204
r_mcangle_it	2.163
r_mcbond_it	1.348
r_angle_refined_deg	1.151
r_nbtor_refined	0.296
r_symmetry_hbond_refined	0.231
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.167
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9854
Nucleic Acid Atoms
Solvent Atoms	714
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection