4S3A | pdb_00004s3a

IspG in complex with Intermediate I

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4S38

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M BIS-TRIS PROPANE, 20% PEG3350, 0.2 M Na2SO4 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.53	α = 90
b = 61.63	β = 127.03
c = 86.16	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	PIXEL	PSI PILATUS 6M		2014-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	30	98.8	0.041	15	3	61825	61083	2	2

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	1.6	1.7	98.9		0.45	2.5

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 (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	4S38	1.6	10	61082	58027	3055	99.13	0.12092	0.11882	0.12	0.16014	0.16	RANDOM	26.484

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]
-0.73		-0.39	1.57		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.629
r_sphericity_free	32.672
r_dihedral_angle_4_deg	18.875
r_sphericity_bonded	15.873
r_dihedral_angle_3_deg	13.837
r_scangle_other	7.2
r_long_range_B_refined	6.707
r_long_range_B_other	6.707
r_scbond_it	6.147
r_scbond_other	6.144
r_dihedral_angle_1_deg	5.45
r_mcangle_it	4.696
r_mcangle_other	4.696
r_mcbond_it	3.719
r_mcbond_other	3.71
r_rigid_bond_restr	3.256
r_angle_refined_deg	2.423
r_angle_other_deg	1.335
r_chiral_restr	0.134
r_bond_refined_d	0.013
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	3076
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	36

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing