2PV7 | pdb_00002pv7

Crystal structure of chorismate mutase / prephenate dehydrogenase (tyrA) (1574749) from Haemophilus influenzae RD at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	NANODROP, 0.04M Potassium dihydrogen phosphate, 20.0% Glycerol, 16.0% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.79	α = 90
b = 127.79	β = 90
c = 100.62	γ = 90

Symmetry
Space Group	P 41 21 2

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 325 mm CCD	Flat mirror (vertical focusing)	2007-04-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97920	SSRL	BL11-1

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	29.696	99.7	0.062	12.89	7.29		56593			32.83

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	2.07	99.3		0.507	2.56		9589

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	29.696	56541	2870	99.75	0.163	0.163	0.161	0.17	0.194	0.2	RANDOM	31.26

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]
0.36			0.36		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.471
r_dihedral_angle_4_deg	20.377
r_dihedral_angle_3_deg	12.801
r_scangle_it	6.309
r_dihedral_angle_1_deg	5.621
r_scbond_it	4.926
r_mcangle_it	2.961
r_mcbond_it	2.189
r_angle_refined_deg	1.61
r_angle_other_deg	0.9
r_mcbond_other	0.586
r_symmetry_vdw_other	0.225
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.187
r_nbtor_refined	0.179
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.149
r_symmetry_vdw_refined	0.104
r_chiral_restr	0.094
r_nbtor_other	0.085
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	4427
Nucleic Acid Atoms
Solvent Atoms	393
Heterogen Atoms	114

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing