Experiment: 5E9P

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	293	1.5 M Sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.517	α = 90
b = 58.517	β = 90
c = 33.437	γ = 90

Symmetry
Space Group	P 43

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		2012-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.2	30	97.9	0.039	0.042	28.7	7.3		34847		-3	15.377

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.3	92.5		0.345	0.375	5.37	6.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5e9o	1.2	30	33108	1739	97.85	0.1066	0.1056	0.1249	RANDOM	14.336

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]
-0.11			-0.11		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	38.088
r_sphericity_free	33.83
r_dihedral_angle_2_deg	32.366
r_sphericity_bonded	16.004
r_dihedral_angle_3_deg	10.727
r_dihedral_angle_1_deg	7.107
r_rigid_bond_restr	6.573
r_mcangle_it	2.582
r_angle_refined_deg	2.13
r_mcbond_it	1.971

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	38.088
r_sphericity_free	33.83
r_dihedral_angle_2_deg	32.366
r_sphericity_bonded	16.004
r_dihedral_angle_3_deg	10.727
r_dihedral_angle_1_deg	7.107
r_rigid_bond_restr	6.573
r_mcangle_it	2.582
r_angle_refined_deg	2.13
r_mcbond_it	1.971
r_mcbond_other	1.935
r_angle_other_deg	1.098
r_chiral_restr	0.132
r_bond_refined_d	0.025
r_gen_planes_refined	0.014
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	715
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	14

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.